Fiona McKenzie - Academia.edu (original) (raw)

Papers by Fiona McKenzie

Research paper thumbnail of A flexible computational pipeline for research analyses of unsolved clinical exome cases

npj Genomic Medicine, 2020

Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial... more Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial diagnostic rates of ~25−30%. Here we develop a robust computational pipeline to rank variants for reassessment of unsolved rare disease patients. A comprehensive web-based patient report is generated in which all deleterious variants can be filtered by gene, variant characteristics, OMIM disease and Phenolyzer scores, and all are annotated with an ACMG classification and links to ClinVar. The pipeline ranked 21/34 previously diagnosed variants as top, with 26 in total ranked ≤7th, 3 ranked ≥13th; 5 failed the pipeline filters. Pathogenic/likely pathogenic variants by ACMG criteria were identified for 22/145 unsolved cases, and a previously undefined candidate disease variant for 27/145. This open access pipeline supports the partnership between clinical and research laboratories to improve the diagnosis of unsolved exomes. It provides a flexible framework for iterative developments to f...

Research paper thumbnail of A clinical scoring system for congenital contractural arachnodactyly

Genetics in Medicine, 2019

Purpose: Congenital contractural arachnodactyly (CCA) is an autosomal dominant connective tissue ... more Purpose: Congenital contractural arachnodactyly (CCA) is an autosomal dominant connective tissue disorder manifesting joint contractures, arachnodactyly, crumpled ears, and kyphoscoliosis as main features. Due to its rarity, rather aspecific clinical presentation, and overlap with other conditions including Marfan syndrome, the diagnosis is challenging, but important for prognosis and clinical management. CCA is caused by pathogenic variants in FBN2, encoding fibrillin-2, but locus heterogeneity has been suggested. We designed a clinical scoring system and diagnostic criteria to support the diagnostic process and guide molecular genetic testing. Methods: In this retrospective study, we assessed 167 probands referred for FBN2 analysis and classified them into a FBN2-positive (n = 44) and FBN2-negative group (n = 123) following molecular analysis. We developed a 20-point weighted clinical scoring system based on the prevalence of ten main clinical characteristics of CCA in both groups. Results: The total score was significantly different between the groups (P < 0.001) and was indicative for classifying patients into unlikely CCA (total score <7) and likely CCA (total score ≥7) groups. Conclusions: Our clinical score is helpful for clinical guidance for patients suspected to have CCA, and provides a quantitative tool for phenotyping in research settings.

Research paper thumbnail of 14q12 microdeletions excluding FOXG1 give rise to a congenital variant Rett syndrome-like phenotype

European Journal of Human Genetics, 2012

Rett syndrome is a clinically defined neurodevelopmental disorder almost exclusively affecting fe... more Rett syndrome is a clinically defined neurodevelopmental disorder almost exclusively affecting females. Usually sporadic, Rett syndrome is caused by mutations in the X-linked MECP2 gene in B90-95% of classic cases and 40-60% of individuals with atypical Rett syndrome. Mutations in the CDKL5 gene have been associated with the early-onset seizure variant of Rett syndrome and mutations in FOXG1 have been associated with the congenital Rett syndrome variant. We report the clinical features and array CGH findings of three atypical Rett syndrome patients who had severe intellectual impairment, early-onset developmental delay, postnatal microcephaly and hypotonia. In addition, the females had a seizure disorder, agenesis of the corpus callosum and subtle dysmorphism. All three were found to have an interstitial deletion of 14q12. The deleted region in common included the PRKD1 gene but not the FOXG1 gene. Gene expression analysis suggested a decrease in FOXG1 levels in two of the patients. Screening of 32 atypical Rett syndrome patients did not identify any pathogenic mutations in the PRKD1 gene, although a previously reported frameshift mutation affecting FOXG1 (c.256dupC, p.Gln86ProfsX35) was identified in a patient with the congenital Rett syndrome variant. There is phenotypic overlap between congenital Rett syndrome variants with FOXG1 mutations and the clinical presentation of our three patients with this 14q12 microdeletion, not encompassing the FOXG1 gene. We propose that the primary defect in these patients is misregulation of the FOXG1 gene rather than a primary abnormality of PRKD1.

Research paper thumbnail of The IFITM5 mutation c.-14C > T results in an elongated transcript expressed in human bone; and causes varying phenotypic severity of osteogenesis imperfecta type V

BMC Musculoskeletal Disorders, 2014

Background The genetic mutation resulting in osteogenesis imperfecta (OI) type V was recently cha... more Background The genetic mutation resulting in osteogenesis imperfecta (OI) type V was recently characterised as a single point mutation (c.-14C > T) in the 5’ untranslated region (UTR) of IFITM5, a gene encoding a transmembrane protein with expression restricted to skeletal tissue. This mutation creates an alternative start codon and has been shown in a eukaryotic cell line to result in a longer variant of IFITM5, but its expression has not previously been demonstrated in bone from a patient with OI type V. Methods Sanger sequencing of the IFITM5 5’ UTR was performed in our cohort of subjects with a clinical diagnosis of OI type V. Clinical data was collated from referring clinicians. RNA was extracted from a bone sample from one patient and Sanger sequenced to determine expression of wild-type and mutant IFITM5. Results All nine subjects with OI type V were heterozygous for the c.-14C > T IFITM5 mutation. Clinically, there was heterogeneity in phenotype, particularly in the ma...

Research paper thumbnail of Endocrine and Growth Abnormalities in 4H Leukodystrophy Caused by Variants in POLR3A, POLR3B, and POLR1C

The Journal of Clinical Endocrinology & Metabolism

Context 4H or POLR3-related leukodystrophy is an autosomal recessive disorder typically character... more Context 4H or POLR3-related leukodystrophy is an autosomal recessive disorder typically characterized by hypomyelination, hypodontia, and hypogonadotropic hypogonadism, caused by biallelic pathogenic variants in POLR3A, POLR3B, POLR1C, and POLR3K. The endocrine and growth abnormalities associated with this disorder have not been thoroughly investigated to date. Objective To systematically characterize endocrine abnormalities of patients with 4H leukodystrophy. Design An international cross-sectional study was performed on 150 patients with genetically confirmed 4H leukodystrophy between 2015 and 2016. Endocrine and growth abnormalities were evaluated, and neurological and other non-neurological features were reviewed. Potential genotype/phenotype associations were also investigated. Setting This was a multicenter retrospective study using information collected from 3 predominant centers. Patients A total of 150 patients with 4H leukodystrophy and pathogenic variants in POLR3A, POLR3...

Research paper thumbnail of Readiness of clinical genetic healthcare professionals to provide genomic medicine: An Australian census

Journal of Genetic Counseling

We aimed to determine capacity and readiness of Australian clinical genetic healthcare profession... more We aimed to determine capacity and readiness of Australian clinical genetic healthcare professionals to provide genomic medicine. An online survey was administered to individuals with genetic counseling or clinical genetics qualifications in Australia. Data collected included: education, certification, continuing professional development (CPD), employment, and genetic versus genomic clinical practice. Of the estimated 630 clinical genetic healthcare professionals in Australia, 354 completed the survey (56.2% response rate). Explanatory interviews were conducted with 5.5% of the genetic counselor respondents. Those working clinically reported being involved in aspects of whole exome or genome sequencing (48.6% genetic counselors, 88.6% clinical geneticists). Most genetic counselors (74.2%) and clinical geneticists (87.0%) had attended genomics CPD in the last two years, with 61.0% and 39.1% self‐funding, respectively. Genetic counselors desire broad involvement in genomics, including understanding classifying and interpreting results to better counsel patients. The majority of respondents (89.9%) were satisfied with their job and 91.6% planned to work in genetics until retirement. However, 14.1% of the genetic counselors in clinical roles and 24.6% of the clinical geneticists planned to retire within 10 years. This is the first national audit of clinical genetic healthcare professionals, revealing the Australian workforce is motivated and prepared to embrace new models to deliver genomic medicine but consideration of education and training is required to meet demand.

Research paper thumbnail of Refining the phenotype associated with GNB1 mutations: Clinical data on 18 newly identified patients and review of the literature

American journal of medical genetics. Part A, Jan 8, 2018

De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To d... more De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To date, 28 patients with variants classified as pathogenic have been reported. We add 18 patients with de novo mutations to this cohort, including a patient with mosaicism for a GNB1 mutation who presented with a milder phenotype. Consistent with previous reports, developmental delay in these patients was moderate to severe, and more than half of the patients were non-ambulatory and nonverbal. The most observed substitution affects the p.Ile80 residue encoded in exon 6, with 28% of patients carrying a variant at this residue. Dystonia and growth delay were observed more frequently in patients carrying variants in this residue, suggesting a potential genotype-phenotype correlation. In the new cohort of 18 patients, 50% of males had genitourinary anomalies and 61% of patients had gastrointestinal anomalies, suggesting a possible association of these findings with variants in GNB1. In addition...

Research paper thumbnail of Elucidating the genetic architecture of Adams-Oliver syndrome in a large European cohort

Human mutation, Jan 20, 2018

Adams-Oliver syndrome (AOS) is a rare developmental disorder, characterized by scalp aplasia cuti... more Adams-Oliver syndrome (AOS) is a rare developmental disorder, characterized by scalp aplasia cutis congenita (ACC) and transverse terminal limb defects (TTLD). Autosomal dominant forms of AOS are linked to mutations in ARHGAP31, DLL4, NOTCH1 or RBPJ, while DOCK6 and EOGT underlie autosomal recessive inheritance. Data on the frequency and distribution of mutations in large cohorts is currently limited. The purpose of this study was therefore to comprehensively examine the genetic architecture of AOS in an extensive cohort. Molecular diagnostic screening of 194 AOS/ACC/TTLD probands/families was conducted using next-generation and/or capillary sequencing analyses. In total, we identified 63 (likely) pathogenic mutations, comprising 56 distinct and 22 novel mutations, providing a molecular diagnosis in 30% of patients. Taken together with previous reports, these findings bring the total number of reported disease variants to 63, with a diagnostic yield of 36% in familial cases. NOTCH1 ...

Research paper thumbnail of Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

Advances in experimental medicine and biology, 2017

Public health relies on technologies to produce and analyse data, as well as effectively develop ... more Public health relies on technologies to produce and analyse data, as well as effectively develop and implement policies and practices. An example is the public health practice of epidemiology, which relies on computational technology to monitor the health status of populations, identify disadvantaged or at risk population groups and thereby inform health policy and priority setting. Critical to achieving health improvements for the underserved population of people living with rare diseases is early diagnosis and best care. In the rare diseases field, the vast majority of diseases are caused by destructive but previously difficult to identify protein-coding gene mutations. The reduction in cost of genetic testing and advances in the clinical use of genome sequencing, data science and imaging are converging to provide more precise understandings of the 'person-time-place' triad. That is: who is affected (people); when the disease is occurring (time); and where the disease is o...

Research paper thumbnail of A craniosynostosis massively parallel sequencing panel study in 309 Australian and New Zealand patients: findings and recommendations

Genetics in medicine : official journal of the American College of Medical Genetics, Sep 7, 2017

PurposeThe craniosynostoses are characterized by premature fusion of one or more cranial sutures.... more PurposeThe craniosynostoses are characterized by premature fusion of one or more cranial sutures. The relative contribution of previously reported genes to craniosynostosis in large cohorts is unclear. Here we report on the use of a massively parallel sequencing panel in individuals with craniosynostosis without a prior molecular diagnosis.MethodsA 20-gene panel was designed based on the genes' association with craniosynostosis, and clinically validated through retrospective testing of an Australian and New Zealand cohort of 233 individuals with craniosynostosis in whom previous testing had not identified a causative variant within FGFR1-3 hot-spot regions or the TWIST1 gene. An additional 76 individuals were tested prospectively.ResultsPathogenic or likely pathogenic variants in non-FGFR genes were identified in 43 individuals, with diagnostic yields of 14% and 15% in retrospective and prospective cohorts, respectively. Variants were identified most frequently in TCF12 (N = 22)...

Research paper thumbnail of A genotype-first approach identifies an intellectual disability-overweight syndrome caused by PHIP haploinsufficiency

European journal of human genetics : EJHG, Jan 5, 2017

Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetic... more Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetics, especially in the era of next generation sequencing. This combines the identification of individuals with mutations in the same gene and linking these to consistent (endo)phenotypes to establish disease causality. We have performed a MIP (molecular inversion probe)-based targeted re-sequencing study in 3,275 individuals with intellectual disability (ID) to facilitate a genotype-first approach for 24 genes previously implicated in ID.Combining our data with data from a publicly available database, we confirmed 11 of these 24 genes to be relevant for ID. Amongst these, PHIP was shown to have an enrichment of disruptive mutations in the individuals with ID (5 out of 3,275). Through international collaboration, we identified a total of 23 individuals with PHIP mutations and elucidated the associated phenotype. Remarkably, all 23 individuals had developmental delay/ID and the majority were...

Research paper thumbnail of Initiating an undiagnosed diseases program in the Western Australian public health system

Orphanet journal of rare diseases, May 3, 2017

New approaches are required to address the needs of complex undiagnosed diseases patients. These ... more New approaches are required to address the needs of complex undiagnosed diseases patients. These approaches include clinical genomic diagnostic pipelines, utilizing intra- and multi-disciplinary platforms, as well as specialty-specific genomic clinics. Both are advancing diagnostic rates. However, complementary cross-disciplinary approaches are also critical to address those patients with multisystem disorders who traverse the bounds of multiple specialties and remain undiagnosed despite existing intra-specialty and genomic-focused approaches. The diagnostic possibilities of undiagnosed diseases include genetic and non-genetic conditions. The focus on genetic diseases addresses some of these disorders, however a cross-disciplinary approach is needed that also simultaneously addresses other disorder types. Herein, we describe the initiation and summary outcomes of a public health system approach for complex undiagnosed patients - the Undiagnosed Diseases Program-Western Australia (UD...

Research paper thumbnail of Short stature and hypoparathyroidism in a child with Kenny-Caffey syndrome type 2 due to a novel mutation in FAM111A gene

International journal of pediatric endocrinology, 2017

Hypoparathyroidism in children is a heterogeneous group with diverse genetic etiologies. To aid c... more Hypoparathyroidism in children is a heterogeneous group with diverse genetic etiologies. To aid clinicians in the investigation and management of children with hypoparathyroidism, we describe the phenotype of a 6-year-old child with hypoparathyroidism and short stature diagnosed with Kenny-Caffey syndrome (KCS) Type 2 and the subsequent response to growth hormone (GH) treatment. The proband presented in the neonatal period with hypocalcemic seizures secondary to hypoparathyroidism. Her phenotype included small hands and feet, hypoplastic and dystrophic nails, hypoplastic mid-face and macrocrania. Postnatal growth was delayed but neurodevelopment was normal. A skeletal survey at 2 years of age was suggestive of KCS Type 2 and genetic testing revealed a novel de novo heterozygous mutation c.1622C > A (p.Ser541Tyr) in FAM111A. At 3 years and 2 months, her height was 80cms (SDS -3.86). She had normal overnight GH levels. GH therapy was commenced at a dose of 4.9 mg/m(2)/week for her ...

Research paper thumbnail of Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

Genome biology, Nov 29, 2016

Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or ph... more Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis. To address this we have developed a massively parallel sequencing targeted DSD gene panel which allows us to sequence all 64 known diagnostic DSD genes and candidate genes simultaneously. We analyzed DNA from the largest reported international cohort of patients with DSD (278 patients with 46,XY DSD and 48 with 46,XX DSD). Our targeted gene panel compares favorably with other sequencing platforms. We found a total of 28 diagnostic genes that are implicated in DSD, highlighting the genetic spectrum of this disorder. Sequencing revealed 93 previously unreported DSD gene variants. Overall, we identified a likely genetic diagnosis in 43% of patients with 46,XY DSD. In patients with 46,XY disorders of androgen synthesis and action the genet...

Research paper thumbnail of The rare and undiagnosed diseases diagnostic service – application of massively parallel sequencing in a state-wide clinical service

Orphanet Journal of Rare Diseases, 2016

Background: The Rare and Undiagnosed Diseases Diagnostic Service (RUDDS) refers to a genomic diag... more Background: The Rare and Undiagnosed Diseases Diagnostic Service (RUDDS) refers to a genomic diagnostic platform operating within the Western Australian Government clinical services delivered through Genetic Services of Western Australia (GSWA). GSWA has provided a statewide service for clinical genetic care for 28 years and it serves a population of 2.5 million people across a geographical area of 2.5milion Km 2. Within this context, GSWA has established a clinically integrated genomic diagnostic platform in partnership with other public health system managers and service providers, including but not limited to the Office of Population Health Genomics, Diagnostic Genomics (PathWest Laboratories) and with executive level support from the Department of Health. Herein we describe report presents the components of this service that are most relevant to the heterogeneity of paediatric clinical genetic care. Results: Briefly the platform : i) offers multiple options including non-genetic testing; monogenic and genomic (targeted in silico filtered and whole exome) analysis; and matchmaking; ii) is delivered in a patient-centric manner that is resonant with the patient journey, it has multiple points for entry, exit and re-entry to allow people access to information they can use, when they want to receive it; iii) is synchronous with precision phenotyping methods; iv) captures new knowledge, including multiple expert review; v) is integrated with current translational genomic research activities and best practice; and vi) is designed for flexibility for interactive generation of, and integration with, clinical research for diagnostics, community engagement, policy and models of care. Conclusion: The RUDDS has been established as part of routine clinical genetic services and is thus sustainable, equitably managed and seeks to translate new knowledge into efficient diagnostics and improved health for the whole community.

Research paper thumbnail of Autosomal dominant Kenny-Caffey syndrome with congenital hypoparathyroidism, short stature and normal intellect: a case report

International Journal of Pediatric Endocrinology, 2015

Research paper thumbnail of Whole exome sequencing is an efficient, sensitive and specific method for determining the genetic cause of short-rib thoracic dystrophies

Clinical Genetics, 2014

Short-rib thoracic dystrophies (SRTDs) are congenital disorders due to defects in primary cilium ... more Short-rib thoracic dystrophies (SRTDs) are congenital disorders due to defects in primary cilium function. SRTDs are recessively inherited with mutations identified in thirteen genes to date (398 exons). Conventional mutation detection (usually by iterative Sanger sequencing) is thus inefficient and expensive, and often not undertaken clinically. Whole exome massive parallel sequencing (WES) has been used to identify new genes for SRTD (WDR34, WDR60 and IFT172); however, the clinical utility of WES has not been established. WES was performed in eleven individuals with SRTDs. Compound heterozygous or homozygous mutations were identified in six known SRTD genes in ten individuals (IFT172, DYNC2H1, TTC21B, WDR60, WDR34 and NEK1), giving overall sensitivity of 90.9%. WES data from 993 unaffected individuals sequenced using similar technology demonstrated two individuals with rare (minor allele frequency &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;0.005) compound heterozygous variants of unknown significance in SRTD genes (specificity &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;99%). Costs for consumables, laboratory processing and bioinformatic analysis were &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;AU$850 per person. WES is sensitive, specific, efficient and cost-effective for mutation screening as well as gene discovery in SRTDs and should be considered a first-line methodology for mutation identification in affected individuals.

Research paper thumbnail of Prenatal Diagnosis of congenital disorder of glycosylation type Ia (CDG-Ia) by cordocentesis and transferrin isoelectric focussing of serum of a 27-week fetus with non-immune hydrops

Prenatal Diagnosis, 2006

Blood was obtained by cordocentesis from a fetus with non-immune hydrops demonstrated by ultrasou... more Blood was obtained by cordocentesis from a fetus with non-immune hydrops demonstrated by ultrasound scanning at 27 weeks' gestation. Abnormalities of serum transferrin isoelectric focussing (IEF) were identified, characteristic of a congenital disorder of glycosylation type I (CDG-Ia). A diagnosis of CDG-Ia was confirmed by enzyme analysis of cultured amniocytes. This is the first report of CDG-Ia diagnosed by serum analysis in a fetus. Previous reports have warned that diagnostic abnormalities do not appear in serum until several weeks after birth. The sensitivity of cordocentesis transferrin IEF is unknown but is less than 100% effective because cases have been diagnosed postnatally after normal prenatal or neonatal studies. Enzyme analysis or mutation analysis is required for diagnosis of congenital disorder of glycosylation (CDGs) regardless of whether a diagnostic transferrin pattern is identified prenatally. The analysis of a small sample of serum, from cordocentesis, performed to check for fetal anemia, simplified the investigation, diagnosis, and genetic counselling of a case of non-immune hydrops detected at 27 weeks' gestation. This might be a useful test for other cases in these circumstances, as fetal blood is usually collected to check for anemia.

Research paper thumbnail of Cardiac homeobox gene NKX2-5 mutations and congenital heart disease

Journal of the American College of Cardiology, 2003

Research paper thumbnail of GM1 gangliosidosis: molecular analysis of nine patients and development of an RT-PCR assay for GLB1 gene expression profiling

Human Mutation, 2007

The human GLB1 gene produces two alternatively spliced transcripts that encode the lysosomal enzy... more The human GLB1 gene produces two alternatively spliced transcripts that encode the lysosomal enzyme β-galactosidase (GLB1) and the elastin binding protein (EBP). Mutations at the GLB1 locus, which are responsible for the storage disorder GM1 gangliosidosis, may affect either both proteins or GLB1 only. The EBP, when affected, contributes to specific features of GM1 gangliosidosis patients, such as cardiomyopathy and connective-tissue abnormalities. Here we report the development of reliable and quantitative assays based on real-time PCR for assessing the levels of GLB1 and EBP transcripts in patients' samples. We also report the characterisation of GLB1 gene mutations in nine GM1 gangliosidosis patients in order to correlate the genetic lesions with mRNA levels and phenotypes. Mutation analysis identified four new (c.1835_1836delCC; p.Arg148Cys; c.1068+1G>T; and p.Pro549Leu), five known (p.Arg59His; p.Arg201His; p.Gly123Arg; c.245+1G>A; and c.75+2insT) mutations and one new polymorphism (c.1233+8T>C). Comparative analysis of the patients' phenotypes enabled a more thorough correlation between GLB1 mutations and specific clinical manifestations. GLB1 and EBP mRNA levels were both reduced in three patients carrying the splicing defects. The accurate and fast method for the detection of alternatively spliced transcripts of the GLB1 gene could be applied to other disease-causing lysosomal genes that encode multiple mRNAs.

Research paper thumbnail of A flexible computational pipeline for research analyses of unsolved clinical exome cases

npj Genomic Medicine, 2020

Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial... more Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial diagnostic rates of ~25−30%. Here we develop a robust computational pipeline to rank variants for reassessment of unsolved rare disease patients. A comprehensive web-based patient report is generated in which all deleterious variants can be filtered by gene, variant characteristics, OMIM disease and Phenolyzer scores, and all are annotated with an ACMG classification and links to ClinVar. The pipeline ranked 21/34 previously diagnosed variants as top, with 26 in total ranked ≤7th, 3 ranked ≥13th; 5 failed the pipeline filters. Pathogenic/likely pathogenic variants by ACMG criteria were identified for 22/145 unsolved cases, and a previously undefined candidate disease variant for 27/145. This open access pipeline supports the partnership between clinical and research laboratories to improve the diagnosis of unsolved exomes. It provides a flexible framework for iterative developments to f...

Research paper thumbnail of A clinical scoring system for congenital contractural arachnodactyly

Genetics in Medicine, 2019

Purpose: Congenital contractural arachnodactyly (CCA) is an autosomal dominant connective tissue ... more Purpose: Congenital contractural arachnodactyly (CCA) is an autosomal dominant connective tissue disorder manifesting joint contractures, arachnodactyly, crumpled ears, and kyphoscoliosis as main features. Due to its rarity, rather aspecific clinical presentation, and overlap with other conditions including Marfan syndrome, the diagnosis is challenging, but important for prognosis and clinical management. CCA is caused by pathogenic variants in FBN2, encoding fibrillin-2, but locus heterogeneity has been suggested. We designed a clinical scoring system and diagnostic criteria to support the diagnostic process and guide molecular genetic testing. Methods: In this retrospective study, we assessed 167 probands referred for FBN2 analysis and classified them into a FBN2-positive (n = 44) and FBN2-negative group (n = 123) following molecular analysis. We developed a 20-point weighted clinical scoring system based on the prevalence of ten main clinical characteristics of CCA in both groups. Results: The total score was significantly different between the groups (P < 0.001) and was indicative for classifying patients into unlikely CCA (total score <7) and likely CCA (total score ≥7) groups. Conclusions: Our clinical score is helpful for clinical guidance for patients suspected to have CCA, and provides a quantitative tool for phenotyping in research settings.

Research paper thumbnail of 14q12 microdeletions excluding FOXG1 give rise to a congenital variant Rett syndrome-like phenotype

European Journal of Human Genetics, 2012

Rett syndrome is a clinically defined neurodevelopmental disorder almost exclusively affecting fe... more Rett syndrome is a clinically defined neurodevelopmental disorder almost exclusively affecting females. Usually sporadic, Rett syndrome is caused by mutations in the X-linked MECP2 gene in B90-95% of classic cases and 40-60% of individuals with atypical Rett syndrome. Mutations in the CDKL5 gene have been associated with the early-onset seizure variant of Rett syndrome and mutations in FOXG1 have been associated with the congenital Rett syndrome variant. We report the clinical features and array CGH findings of three atypical Rett syndrome patients who had severe intellectual impairment, early-onset developmental delay, postnatal microcephaly and hypotonia. In addition, the females had a seizure disorder, agenesis of the corpus callosum and subtle dysmorphism. All three were found to have an interstitial deletion of 14q12. The deleted region in common included the PRKD1 gene but not the FOXG1 gene. Gene expression analysis suggested a decrease in FOXG1 levels in two of the patients. Screening of 32 atypical Rett syndrome patients did not identify any pathogenic mutations in the PRKD1 gene, although a previously reported frameshift mutation affecting FOXG1 (c.256dupC, p.Gln86ProfsX35) was identified in a patient with the congenital Rett syndrome variant. There is phenotypic overlap between congenital Rett syndrome variants with FOXG1 mutations and the clinical presentation of our three patients with this 14q12 microdeletion, not encompassing the FOXG1 gene. We propose that the primary defect in these patients is misregulation of the FOXG1 gene rather than a primary abnormality of PRKD1.

Research paper thumbnail of The IFITM5 mutation c.-14C > T results in an elongated transcript expressed in human bone; and causes varying phenotypic severity of osteogenesis imperfecta type V

BMC Musculoskeletal Disorders, 2014

Background The genetic mutation resulting in osteogenesis imperfecta (OI) type V was recently cha... more Background The genetic mutation resulting in osteogenesis imperfecta (OI) type V was recently characterised as a single point mutation (c.-14C > T) in the 5’ untranslated region (UTR) of IFITM5, a gene encoding a transmembrane protein with expression restricted to skeletal tissue. This mutation creates an alternative start codon and has been shown in a eukaryotic cell line to result in a longer variant of IFITM5, but its expression has not previously been demonstrated in bone from a patient with OI type V. Methods Sanger sequencing of the IFITM5 5’ UTR was performed in our cohort of subjects with a clinical diagnosis of OI type V. Clinical data was collated from referring clinicians. RNA was extracted from a bone sample from one patient and Sanger sequenced to determine expression of wild-type and mutant IFITM5. Results All nine subjects with OI type V were heterozygous for the c.-14C > T IFITM5 mutation. Clinically, there was heterogeneity in phenotype, particularly in the ma...

Research paper thumbnail of Endocrine and Growth Abnormalities in 4H Leukodystrophy Caused by Variants in POLR3A, POLR3B, and POLR1C

The Journal of Clinical Endocrinology & Metabolism

Context 4H or POLR3-related leukodystrophy is an autosomal recessive disorder typically character... more Context 4H or POLR3-related leukodystrophy is an autosomal recessive disorder typically characterized by hypomyelination, hypodontia, and hypogonadotropic hypogonadism, caused by biallelic pathogenic variants in POLR3A, POLR3B, POLR1C, and POLR3K. The endocrine and growth abnormalities associated with this disorder have not been thoroughly investigated to date. Objective To systematically characterize endocrine abnormalities of patients with 4H leukodystrophy. Design An international cross-sectional study was performed on 150 patients with genetically confirmed 4H leukodystrophy between 2015 and 2016. Endocrine and growth abnormalities were evaluated, and neurological and other non-neurological features were reviewed. Potential genotype/phenotype associations were also investigated. Setting This was a multicenter retrospective study using information collected from 3 predominant centers. Patients A total of 150 patients with 4H leukodystrophy and pathogenic variants in POLR3A, POLR3...

Research paper thumbnail of Readiness of clinical genetic healthcare professionals to provide genomic medicine: An Australian census

Journal of Genetic Counseling

We aimed to determine capacity and readiness of Australian clinical genetic healthcare profession... more We aimed to determine capacity and readiness of Australian clinical genetic healthcare professionals to provide genomic medicine. An online survey was administered to individuals with genetic counseling or clinical genetics qualifications in Australia. Data collected included: education, certification, continuing professional development (CPD), employment, and genetic versus genomic clinical practice. Of the estimated 630 clinical genetic healthcare professionals in Australia, 354 completed the survey (56.2% response rate). Explanatory interviews were conducted with 5.5% of the genetic counselor respondents. Those working clinically reported being involved in aspects of whole exome or genome sequencing (48.6% genetic counselors, 88.6% clinical geneticists). Most genetic counselors (74.2%) and clinical geneticists (87.0%) had attended genomics CPD in the last two years, with 61.0% and 39.1% self‐funding, respectively. Genetic counselors desire broad involvement in genomics, including understanding classifying and interpreting results to better counsel patients. The majority of respondents (89.9%) were satisfied with their job and 91.6% planned to work in genetics until retirement. However, 14.1% of the genetic counselors in clinical roles and 24.6% of the clinical geneticists planned to retire within 10 years. This is the first national audit of clinical genetic healthcare professionals, revealing the Australian workforce is motivated and prepared to embrace new models to deliver genomic medicine but consideration of education and training is required to meet demand.

Research paper thumbnail of Refining the phenotype associated with GNB1 mutations: Clinical data on 18 newly identified patients and review of the literature

American journal of medical genetics. Part A, Jan 8, 2018

De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To d... more De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To date, 28 patients with variants classified as pathogenic have been reported. We add 18 patients with de novo mutations to this cohort, including a patient with mosaicism for a GNB1 mutation who presented with a milder phenotype. Consistent with previous reports, developmental delay in these patients was moderate to severe, and more than half of the patients were non-ambulatory and nonverbal. The most observed substitution affects the p.Ile80 residue encoded in exon 6, with 28% of patients carrying a variant at this residue. Dystonia and growth delay were observed more frequently in patients carrying variants in this residue, suggesting a potential genotype-phenotype correlation. In the new cohort of 18 patients, 50% of males had genitourinary anomalies and 61% of patients had gastrointestinal anomalies, suggesting a possible association of these findings with variants in GNB1. In addition...

Research paper thumbnail of Elucidating the genetic architecture of Adams-Oliver syndrome in a large European cohort

Human mutation, Jan 20, 2018

Adams-Oliver syndrome (AOS) is a rare developmental disorder, characterized by scalp aplasia cuti... more Adams-Oliver syndrome (AOS) is a rare developmental disorder, characterized by scalp aplasia cutis congenita (ACC) and transverse terminal limb defects (TTLD). Autosomal dominant forms of AOS are linked to mutations in ARHGAP31, DLL4, NOTCH1 or RBPJ, while DOCK6 and EOGT underlie autosomal recessive inheritance. Data on the frequency and distribution of mutations in large cohorts is currently limited. The purpose of this study was therefore to comprehensively examine the genetic architecture of AOS in an extensive cohort. Molecular diagnostic screening of 194 AOS/ACC/TTLD probands/families was conducted using next-generation and/or capillary sequencing analyses. In total, we identified 63 (likely) pathogenic mutations, comprising 56 distinct and 22 novel mutations, providing a molecular diagnosis in 30% of patients. Taken together with previous reports, these findings bring the total number of reported disease variants to 63, with a diagnostic yield of 36% in familial cases. NOTCH1 ...

Research paper thumbnail of Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

Advances in experimental medicine and biology, 2017

Public health relies on technologies to produce and analyse data, as well as effectively develop ... more Public health relies on technologies to produce and analyse data, as well as effectively develop and implement policies and practices. An example is the public health practice of epidemiology, which relies on computational technology to monitor the health status of populations, identify disadvantaged or at risk population groups and thereby inform health policy and priority setting. Critical to achieving health improvements for the underserved population of people living with rare diseases is early diagnosis and best care. In the rare diseases field, the vast majority of diseases are caused by destructive but previously difficult to identify protein-coding gene mutations. The reduction in cost of genetic testing and advances in the clinical use of genome sequencing, data science and imaging are converging to provide more precise understandings of the 'person-time-place' triad. That is: who is affected (people); when the disease is occurring (time); and where the disease is o...

Research paper thumbnail of A craniosynostosis massively parallel sequencing panel study in 309 Australian and New Zealand patients: findings and recommendations

Genetics in medicine : official journal of the American College of Medical Genetics, Sep 7, 2017

PurposeThe craniosynostoses are characterized by premature fusion of one or more cranial sutures.... more PurposeThe craniosynostoses are characterized by premature fusion of one or more cranial sutures. The relative contribution of previously reported genes to craniosynostosis in large cohorts is unclear. Here we report on the use of a massively parallel sequencing panel in individuals with craniosynostosis without a prior molecular diagnosis.MethodsA 20-gene panel was designed based on the genes' association with craniosynostosis, and clinically validated through retrospective testing of an Australian and New Zealand cohort of 233 individuals with craniosynostosis in whom previous testing had not identified a causative variant within FGFR1-3 hot-spot regions or the TWIST1 gene. An additional 76 individuals were tested prospectively.ResultsPathogenic or likely pathogenic variants in non-FGFR genes were identified in 43 individuals, with diagnostic yields of 14% and 15% in retrospective and prospective cohorts, respectively. Variants were identified most frequently in TCF12 (N = 22)...

Research paper thumbnail of A genotype-first approach identifies an intellectual disability-overweight syndrome caused by PHIP haploinsufficiency

European journal of human genetics : EJHG, Jan 5, 2017

Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetic... more Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetics, especially in the era of next generation sequencing. This combines the identification of individuals with mutations in the same gene and linking these to consistent (endo)phenotypes to establish disease causality. We have performed a MIP (molecular inversion probe)-based targeted re-sequencing study in 3,275 individuals with intellectual disability (ID) to facilitate a genotype-first approach for 24 genes previously implicated in ID.Combining our data with data from a publicly available database, we confirmed 11 of these 24 genes to be relevant for ID. Amongst these, PHIP was shown to have an enrichment of disruptive mutations in the individuals with ID (5 out of 3,275). Through international collaboration, we identified a total of 23 individuals with PHIP mutations and elucidated the associated phenotype. Remarkably, all 23 individuals had developmental delay/ID and the majority were...

Research paper thumbnail of Initiating an undiagnosed diseases program in the Western Australian public health system

Orphanet journal of rare diseases, May 3, 2017

New approaches are required to address the needs of complex undiagnosed diseases patients. These ... more New approaches are required to address the needs of complex undiagnosed diseases patients. These approaches include clinical genomic diagnostic pipelines, utilizing intra- and multi-disciplinary platforms, as well as specialty-specific genomic clinics. Both are advancing diagnostic rates. However, complementary cross-disciplinary approaches are also critical to address those patients with multisystem disorders who traverse the bounds of multiple specialties and remain undiagnosed despite existing intra-specialty and genomic-focused approaches. The diagnostic possibilities of undiagnosed diseases include genetic and non-genetic conditions. The focus on genetic diseases addresses some of these disorders, however a cross-disciplinary approach is needed that also simultaneously addresses other disorder types. Herein, we describe the initiation and summary outcomes of a public health system approach for complex undiagnosed patients - the Undiagnosed Diseases Program-Western Australia (UD...

Research paper thumbnail of Short stature and hypoparathyroidism in a child with Kenny-Caffey syndrome type 2 due to a novel mutation in FAM111A gene

International journal of pediatric endocrinology, 2017

Hypoparathyroidism in children is a heterogeneous group with diverse genetic etiologies. To aid c... more Hypoparathyroidism in children is a heterogeneous group with diverse genetic etiologies. To aid clinicians in the investigation and management of children with hypoparathyroidism, we describe the phenotype of a 6-year-old child with hypoparathyroidism and short stature diagnosed with Kenny-Caffey syndrome (KCS) Type 2 and the subsequent response to growth hormone (GH) treatment. The proband presented in the neonatal period with hypocalcemic seizures secondary to hypoparathyroidism. Her phenotype included small hands and feet, hypoplastic and dystrophic nails, hypoplastic mid-face and macrocrania. Postnatal growth was delayed but neurodevelopment was normal. A skeletal survey at 2 years of age was suggestive of KCS Type 2 and genetic testing revealed a novel de novo heterozygous mutation c.1622C > A (p.Ser541Tyr) in FAM111A. At 3 years and 2 months, her height was 80cms (SDS -3.86). She had normal overnight GH levels. GH therapy was commenced at a dose of 4.9 mg/m(2)/week for her ...

Research paper thumbnail of Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

Genome biology, Nov 29, 2016

Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or ph... more Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis. To address this we have developed a massively parallel sequencing targeted DSD gene panel which allows us to sequence all 64 known diagnostic DSD genes and candidate genes simultaneously. We analyzed DNA from the largest reported international cohort of patients with DSD (278 patients with 46,XY DSD and 48 with 46,XX DSD). Our targeted gene panel compares favorably with other sequencing platforms. We found a total of 28 diagnostic genes that are implicated in DSD, highlighting the genetic spectrum of this disorder. Sequencing revealed 93 previously unreported DSD gene variants. Overall, we identified a likely genetic diagnosis in 43% of patients with 46,XY DSD. In patients with 46,XY disorders of androgen synthesis and action the genet...

Research paper thumbnail of The rare and undiagnosed diseases diagnostic service – application of massively parallel sequencing in a state-wide clinical service

Orphanet Journal of Rare Diseases, 2016

Background: The Rare and Undiagnosed Diseases Diagnostic Service (RUDDS) refers to a genomic diag... more Background: The Rare and Undiagnosed Diseases Diagnostic Service (RUDDS) refers to a genomic diagnostic platform operating within the Western Australian Government clinical services delivered through Genetic Services of Western Australia (GSWA). GSWA has provided a statewide service for clinical genetic care for 28 years and it serves a population of 2.5 million people across a geographical area of 2.5milion Km 2. Within this context, GSWA has established a clinically integrated genomic diagnostic platform in partnership with other public health system managers and service providers, including but not limited to the Office of Population Health Genomics, Diagnostic Genomics (PathWest Laboratories) and with executive level support from the Department of Health. Herein we describe report presents the components of this service that are most relevant to the heterogeneity of paediatric clinical genetic care. Results: Briefly the platform : i) offers multiple options including non-genetic testing; monogenic and genomic (targeted in silico filtered and whole exome) analysis; and matchmaking; ii) is delivered in a patient-centric manner that is resonant with the patient journey, it has multiple points for entry, exit and re-entry to allow people access to information they can use, when they want to receive it; iii) is synchronous with precision phenotyping methods; iv) captures new knowledge, including multiple expert review; v) is integrated with current translational genomic research activities and best practice; and vi) is designed for flexibility for interactive generation of, and integration with, clinical research for diagnostics, community engagement, policy and models of care. Conclusion: The RUDDS has been established as part of routine clinical genetic services and is thus sustainable, equitably managed and seeks to translate new knowledge into efficient diagnostics and improved health for the whole community.

Research paper thumbnail of Autosomal dominant Kenny-Caffey syndrome with congenital hypoparathyroidism, short stature and normal intellect: a case report

International Journal of Pediatric Endocrinology, 2015

Research paper thumbnail of Whole exome sequencing is an efficient, sensitive and specific method for determining the genetic cause of short-rib thoracic dystrophies

Clinical Genetics, 2014

Short-rib thoracic dystrophies (SRTDs) are congenital disorders due to defects in primary cilium ... more Short-rib thoracic dystrophies (SRTDs) are congenital disorders due to defects in primary cilium function. SRTDs are recessively inherited with mutations identified in thirteen genes to date (398 exons). Conventional mutation detection (usually by iterative Sanger sequencing) is thus inefficient and expensive, and often not undertaken clinically. Whole exome massive parallel sequencing (WES) has been used to identify new genes for SRTD (WDR34, WDR60 and IFT172); however, the clinical utility of WES has not been established. WES was performed in eleven individuals with SRTDs. Compound heterozygous or homozygous mutations were identified in six known SRTD genes in ten individuals (IFT172, DYNC2H1, TTC21B, WDR60, WDR34 and NEK1), giving overall sensitivity of 90.9%. WES data from 993 unaffected individuals sequenced using similar technology demonstrated two individuals with rare (minor allele frequency &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;0.005) compound heterozygous variants of unknown significance in SRTD genes (specificity &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;99%). Costs for consumables, laboratory processing and bioinformatic analysis were &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;AU$850 per person. WES is sensitive, specific, efficient and cost-effective for mutation screening as well as gene discovery in SRTDs and should be considered a first-line methodology for mutation identification in affected individuals.

Research paper thumbnail of Prenatal Diagnosis of congenital disorder of glycosylation type Ia (CDG-Ia) by cordocentesis and transferrin isoelectric focussing of serum of a 27-week fetus with non-immune hydrops

Prenatal Diagnosis, 2006

Blood was obtained by cordocentesis from a fetus with non-immune hydrops demonstrated by ultrasou... more Blood was obtained by cordocentesis from a fetus with non-immune hydrops demonstrated by ultrasound scanning at 27 weeks' gestation. Abnormalities of serum transferrin isoelectric focussing (IEF) were identified, characteristic of a congenital disorder of glycosylation type I (CDG-Ia). A diagnosis of CDG-Ia was confirmed by enzyme analysis of cultured amniocytes. This is the first report of CDG-Ia diagnosed by serum analysis in a fetus. Previous reports have warned that diagnostic abnormalities do not appear in serum until several weeks after birth. The sensitivity of cordocentesis transferrin IEF is unknown but is less than 100% effective because cases have been diagnosed postnatally after normal prenatal or neonatal studies. Enzyme analysis or mutation analysis is required for diagnosis of congenital disorder of glycosylation (CDGs) regardless of whether a diagnostic transferrin pattern is identified prenatally. The analysis of a small sample of serum, from cordocentesis, performed to check for fetal anemia, simplified the investigation, diagnosis, and genetic counselling of a case of non-immune hydrops detected at 27 weeks' gestation. This might be a useful test for other cases in these circumstances, as fetal blood is usually collected to check for anemia.

Research paper thumbnail of Cardiac homeobox gene NKX2-5 mutations and congenital heart disease

Journal of the American College of Cardiology, 2003

Research paper thumbnail of GM1 gangliosidosis: molecular analysis of nine patients and development of an RT-PCR assay for GLB1 gene expression profiling

Human Mutation, 2007

The human GLB1 gene produces two alternatively spliced transcripts that encode the lysosomal enzy... more The human GLB1 gene produces two alternatively spliced transcripts that encode the lysosomal enzyme β-galactosidase (GLB1) and the elastin binding protein (EBP). Mutations at the GLB1 locus, which are responsible for the storage disorder GM1 gangliosidosis, may affect either both proteins or GLB1 only. The EBP, when affected, contributes to specific features of GM1 gangliosidosis patients, such as cardiomyopathy and connective-tissue abnormalities. Here we report the development of reliable and quantitative assays based on real-time PCR for assessing the levels of GLB1 and EBP transcripts in patients' samples. We also report the characterisation of GLB1 gene mutations in nine GM1 gangliosidosis patients in order to correlate the genetic lesions with mRNA levels and phenotypes. Mutation analysis identified four new (c.1835_1836delCC; p.Arg148Cys; c.1068+1G>T; and p.Pro549Leu), five known (p.Arg59His; p.Arg201His; p.Gly123Arg; c.245+1G>A; and c.75+2insT) mutations and one new polymorphism (c.1233+8T>C). Comparative analysis of the patients' phenotypes enabled a more thorough correlation between GLB1 mutations and specific clinical manifestations. GLB1 and EBP mRNA levels were both reduced in three patients carrying the splicing defects. The accurate and fast method for the detection of alternatively spliced transcripts of the GLB1 gene could be applied to other disease-causing lysosomal genes that encode multiple mRNAs.