Darren Griffin | Universidad de Buenos Aires (original) (raw)

Papers by Darren Griffin

Research paper thumbnail of Additional file 8: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S6. Comparison of frequencies of microsatellite repeat motifs in 22 chicken and zebra finch... more Table S6. Comparison of frequencies of microsatellite repeat motifs in 22 chicken and zebra finch BACs mapped on the Siamese cobra chromosome 1 and microchromosomes. (DOCX 19 kb)

Research paper thumbnail of Additional file 6: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S4. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BA... more Table S4. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BACs mapped on the Siamese cobra chromosome 2. (DOCX 14 kb)

Research paper thumbnail of Additional file 5: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S3. Comparison of major classes of repeat sequences in chicken and zebra finch BACs mapped ... more Table S3. Comparison of major classes of repeat sequences in chicken and zebra finch BACs mapped on the Siamese cobra chromosome 2. (DOCX 15 kb)

Research paper thumbnail of Additional file 4: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S2. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BA... more Table S2. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BACs mapped on the Siamese cobra Z chromosome. (DOCX 13 kb)

Research paper thumbnail of Additional file 1: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent "a hypothetical ancestral super-sex chromosome" or random distribution?

Figure S1. Chromosomal locations of microsatellite repeat motifs in the Siamese cobra (Naja kaout... more Figure S1. Chromosomal locations of microsatellite repeat motifs in the Siamese cobra (Naja kaouthia). Hybridization patterns of FITC-labeled (CA)15 (a), (AT)15 (b), (GC)15 (c), (CAT)10 (d), and (AAT)10 (e) on DAPI-stained chromosomes. Scale bar represents 10 μm. (JPG 175 kb)

Research paper thumbnail of Additional file 2: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

Chromosomal coordinates and orientation of mapped scaffolds and PCFs are listed by chromosome for... more Chromosomal coordinates and orientation of mapped scaffolds and PCFs are listed by chromosome for each species. Data is listed in supplementary tables as follows: Table S4. Ostrich genome; Table S5. Budgerigar genome; Table S6. Saker falcon genome. (ZIP 87 kb)

Research paper thumbnail of Additional file 3: of Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Figure S1.â Day old chicks with the white (A) and yellow (B) down colour. (JPG 586 kb)

Research paper thumbnail of Additional file 1: of Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Table S1. Basic information for SNP markers per chromosome after quality control. (DOCX 29 kb)

Research paper thumbnail of Additional file 1: of Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

Supplementary information, tables and figures. (PDF 781 kb)

Research paper thumbnail of The effects of laser manipulation on biopsy karyotype in PGS

Reproductive BioMedicine Online, 2018

Research paper thumbnail of Comparative chromosome painting in Spizaetus tyrannus and Gallus gallus with the use of macro- and microchromosome probes

PLOS ONE, 2021

Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes... more Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes and many microchromosomes pairs, some groups, such as the Accipitriformes, are characterized by a large karyotypic reorganization, which resulted in complements with low diploid numbers, and a smaller number of microchromosomal pairs when compared to other birds. Among Accipitriformes, the Accipitridae family is the most diverse and includes, among other subfamilies, the subfamily Aquilinae, composed of medium to large sized species. The Black-Hawk-Eagle (Spizaetus tyrannus-STY), found in South America, is a member of this subfamily. Available chromosome data for this species includes only conventional staining. Hence, in order to provide additional information on karyotype evolution process within this group, we performed comparative chromosome painting between S. tyrannus and Gallus gallus (GGA). Our results revealed that at least 29 fission-fusion events occurred in the STY karyotype...

Research paper thumbnail of Revising the Chromosome-Specific Probes of White Hawk (Leucopternis albicollis)

Proceedings, 2020

Leucopternis albicollis is a diurnal bird of prey with extensive karyotype reorganization. Chromo... more Leucopternis albicollis is a diurnal bird of prey with extensive karyotype reorganization. Chromosome-specific probes from this species have been used successfully to detect intrachromosomal rearrangements in different species of bird since 2010. However, some gaps were detected in this first set of probes. Here, we have obtained a new set of whole chromosome probes in order to improve the previous one; also, we have performed experiments using bacterial artificial chromosome (BAC) from chicken microchromosomes. Our results demonstrated that the microchromosomes were involved in fusion events. In addition, a new nomenclature has been proposed for the new set of probes and some inaccurate data were corrected.

Research paper thumbnail of Validating PGS by probing the karyotypic concordance between ICM and TE

Reproductive Biomedicine Online, 2018

Research paper thumbnail of Sample pooling, a population screening strategy for SARS-CoV2 to prevent future outbreak and mitigate the “second-wave” of infection of the virus

medRxiv, 2020

Problem How do we manage treatment and stabilization in clinical settings and static population c... more Problem How do we manage treatment and stabilization in clinical settings and static population communities like assisted living facility settings of their patient or resident populations during and post the SARS-CoV-2 pandemic? Scope This proposal explores the possible and predicted changes to standard operating procedures to the facility management and associated landscape and focuses on series of deployments, during and post peak SARS-CoV-2 activity, and will outline possible models for the current medical facility model that we operate with. This article primarily focuses on non-emergency facility management. Assumptions and understanding of the field With a reduction in the numbers nationally, patients are highly motivated and likely to seek non-emergency and planned medical procedural treatment as early as possible as social distancing measures are eased and restrictions on non-urgent procedures are lifted. Conclusions and next steps An initial pan-national shutdown and suspen...

Research paper thumbnail of Cattle karyomapping to optimise food production and delivery of superior genetics: the first liveborn calves

Research paper thumbnail of PGS: a four-letter word?

The Biochemist, 2018

Preimplantation genetic screening (PGS) involves the identification of chromosome abnormalities i... more Preimplantation genetic screening (PGS) involves the identification of chromosome abnormalities in IVF embryos (rather than targeting diagnosis to a specified gene). Chiefly employed for couples with advanced maternal age, recurrent miscarriage or recurrent IVF failure, it aims to improve IVF success, and reduce miscarriage and affected live birth rates. The process involves the sampling of cells by embryo biopsy, cytogenetic diagnosis, then selective transfer of an apparently chromosomally normal embryo in the hope of establishing a pregnancy. Although PGS is the most common variant of PGD (preimplantation genetic diagnosis), accounting for 80% of cases it has, from the outset, been one of the most controversial areas of reproductive medicine. The subject of intense debate, it attracts opinions ranging from recommendations that it should be applied in all IVF cases, through to the suggestion it should be discontinued completely. What do you think? Should it continue or not?

Research paper thumbnail of Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

Diversity, 2018

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, ... more Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate an...

Research paper thumbnail of Reporting of Mosaics as High-level and Low level mosaics makes more number of embryos available as alternatives for transfer when no euploid embryos are available

Reproductive BioMedicine Online, 2019

Introduction It is relatively common for human preimplantation embryos produced during the course... more Introduction It is relatively common for human preimplantation embryos produced during the course of IVF treatments to contain two or more cytogenetically distinct cell lines. This phenomenon, known as chromosomal mosaicism, can result in either a mixture of euploid and abnormal cells, or abnormal cells bearing distinct chromosomal gains and losses. NGS allows mosaicism to be detected with much greater sensitivity than earlier preimplantation genetic testing (PGT-A) methods. The application of NGS to trophectoderm biopsies, taken from embryos before transfer to the uterus, has provided insight into the clinical impact of mosaicism. However, because some mosaic embryos are have produced successful pregnancies, it may be appropriate to consider transfer of mosaic embryos in the absence of fully euploid embryos and following patient counseling. Materials and Methods Samples were amplified by SurePlex, sequenced with VeriSeq PGS assay (Illumina) on MiSeq (Illumina) and analyzed with BlueFuse Multi analysis (Illumina). Embryos with at least one fully aneuploid chromosome or one fully aneuploid chromosome and one mosaic chromosome were called aneuploid. Embryos with 3 chromosome abnormalities were designated complex abnormal. Mosaicism was reported when embryos had 20-80% abnormal sequencing profiles. Embryos with low degrees of mosaicism in sequencing profiles were designated as ‘Low –Level Mosaics’. When embryos had high degree of mosaicism, they were reported as ‘High- Level Mosaics’. Design Retrospective analysis of PGS procedures involving TE biopsy and NGS performed by laboratories serving over 250 fertility clinics over three years. A total of 3951 embryos resulting from 952 IVF cycles were analyzed. Results Gross aneuploidy (includes complex abnormals and polyploidies) rates in egg donors (n=402) was 25.62%. Euploid rate in egg donors was 51.00%. 20.90% embryos from egg donors were mosaic, with 11.94% being classified as High-level mosaic and 8.96% being classified as Low-level mosaic. In the non-egg donor group (n=3,545 embryos) aneuploidy (includes complex abnormals and polyploidies) ranged at 44.23%. Euploid rate in non-egg donors was about 36.47%. About 15.94% embryos were mosaic with no trend observed in advanced maternal age and mosaicism. About 8% of all embryos in the non-egg donor group were High-level mosaics while and equal percentage of embryos were Low- level mosaics. A total of 33% cycles (n=317 cycles) resulted in cohorts which had zero euploid embryos. Of these 317 cycles however, 112 cycles (35%), had at least one mosaic embryo to transfer. Of the zero-euploid group a total of 52 cycles (16%) resulted in a Low-level mosaic for patients who otherwise do not have any normal/euploid embryos to transfer. Only 7 cycles from the donor group resulted in cohorts with zero euploid embryos. Conclusion The ability of PGT-A by NGS to delineate between high-level and low-level mosaic embryos allows patients without euploid embryos for transfer the ability to identify mosaic embryos with the greatest likelihood of producing a successful pregnancy. Approximately 8% of all embryos tested by PGT-A are low-level mosaic, with 16% of cycles without identified euploid embryos producing at least one low-level mosaic embryo. The results herein can be used to counsel patients and guide expectations.

Research paper thumbnail of Aneuploidy concordance between trophectoderm and inner cell mass by next-generation sequencingin 100 blastocysts

Reproductive BioMedicine Online, 2019

Introduction A number of clinical trials have reported improved IVF outcomes when embryos are pre... more Introduction A number of clinical trials have reported improved IVF outcomes when embryos are previously vetted for chromosomal aneuploidies, and yet a significant percentage of euploid embryos still fail to implant. Conversely, there is mounting evidence of mosaic embryos leading to pregnancies, and there even exist anecdotal reports of aneuploid embryos resulting in healthy births. Critics of PGT- A point out that a TE biopsy might not correctly represent the entire blastocyst. Genetic discordance between TE and ICM could severely affect the clinical outcomes of PGT-A. Furthermore, a blastocyst classified as aneuploidy might in reality contain a euploid ICM, which could lead to discarding potentially viable embryos in IVFclinics. To date, studies addressing the question of concordance between TE and ICM have relied oncurrently superseded technologies and/or small sample sizes. Here we analyze 100 blastocysts that wereclassified as aneuploid by PGT-A, probing the genetic makup of their paired ICMs using high-resolutionNextGen Sequencing (hr-NGS). Materials & methods We optimized a method to collect ICM biopsies that are free of TE cell contamination, validated by immunofluorescence for lineage markers. Using this technique we isolated ICM biopsies from 100 blastocysts that had previously undergone clinical PGT-A, and had displayed aneuploidy in their TE biopsies (93 whole chromosome aneuploids and 7 segmental aneuploids). All samples were analyzed by hr-NGS, and resulting karyotype profiles of TE and ICM biopsies were compared. We also developed a bioinformatics approach based on SNP analysis and imputation to confirm that the biopsies of blastocysts with TE-ICM discordance indeed stemmed from the same embryo, excluding the possibility of sample mix-up or contamination. Results Comparison of 100 paired TE-ICM karyotypes revealed that a clinical TE biopsy correctly predicts aneuploidy in the ICM in the vast majority of cases. When one or more whole chromosomes were aneuploid in the clinical TE biopsy, the corresponding ICM was aneuploid in 90 out of 93 blastocysts (96.8%). Nonetheless, when the clinical TE biopsy only contained segmental (sub- chromosomal) aneuploidies, the ICM was aneuploid in only 3 out of 7 cases (43%). Combined, and when all types of aneuploidy were considered, an aneuploid TE biopsy correctly predicted aneuploidy in the ICM in 93 outof 100 cases. Of the 7 out of 100 blastocysts that were TE-ICM discordant, the ICM was mosaic in 2 casesand euploid in 5 cases. A second TE biopsy collected from the 7 TE-ICM discordant blastocysts showedconcordance with the original clinical TE biopsy in only 2 out of 7 cases (28%). Conclusions These findings suggest that TE biopsy, in our hands, largely predicts the chromosome constitution of the ICM and this has significant clinical implications. Concomitantly, the results suggest clinical value of reevaluatingblastocysts deemed ‘aneuploid’ in select cases by TE re-biopsy, particularly in instances of segmental aneuploidies.

Research paper thumbnail of Physiological, hyaluronan-selected intracytoplasmic sperm injection for infertility treatment (HABSelect): a parallel, two-group, randomised trial

Research paper thumbnail of Additional file 8: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S6. Comparison of frequencies of microsatellite repeat motifs in 22 chicken and zebra finch... more Table S6. Comparison of frequencies of microsatellite repeat motifs in 22 chicken and zebra finch BACs mapped on the Siamese cobra chromosome 1 and microchromosomes. (DOCX 19 kb)

Research paper thumbnail of Additional file 6: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S4. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BA... more Table S4. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BACs mapped on the Siamese cobra chromosome 2. (DOCX 14 kb)

Research paper thumbnail of Additional file 5: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S3. Comparison of major classes of repeat sequences in chicken and zebra finch BACs mapped ... more Table S3. Comparison of major classes of repeat sequences in chicken and zebra finch BACs mapped on the Siamese cobra chromosome 2. (DOCX 15 kb)

Research paper thumbnail of Additional file 4: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent â a hypothetical ancestral super-sex chromosomeâ or random distribution?

Table S2. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BA... more Table S2. Comparison of frequencies of microsatellite repeat motifs in chicken and zebra finch BACs mapped on the Siamese cobra Z chromosome. (DOCX 13 kb)

Research paper thumbnail of Additional file 1: of Chromosome map of the Siamese cobra: did partial synteny of sex chromosomes in the amniote represent "a hypothetical ancestral super-sex chromosome" or random distribution?

Figure S1. Chromosomal locations of microsatellite repeat motifs in the Siamese cobra (Naja kaout... more Figure S1. Chromosomal locations of microsatellite repeat motifs in the Siamese cobra (Naja kaouthia). Hybridization patterns of FITC-labeled (CA)15 (a), (AT)15 (b), (GC)15 (c), (CAT)10 (d), and (AAT)10 (e) on DAPI-stained chromosomes. Scale bar represents 10 μm. (JPG 175 kb)

Research paper thumbnail of Additional file 2: of Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

Chromosomal coordinates and orientation of mapped scaffolds and PCFs are listed by chromosome for... more Chromosomal coordinates and orientation of mapped scaffolds and PCFs are listed by chromosome for each species. Data is listed in supplementary tables as follows: Table S4. Ostrich genome; Table S5. Budgerigar genome; Table S6. Saker falcon genome. (ZIP 87 kb)

Research paper thumbnail of Additional file 3: of Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Figure S1.â Day old chicks with the white (A) and yellow (B) down colour. (JPG 586 kb)

Research paper thumbnail of Additional file 1: of Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Table S1. Basic information for SNP markers per chromosome after quality control. (DOCX 29 kb)

Research paper thumbnail of Additional file 1: of Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

Supplementary information, tables and figures. (PDF 781 kb)

Research paper thumbnail of The effects of laser manipulation on biopsy karyotype in PGS

Reproductive BioMedicine Online, 2018

Research paper thumbnail of Comparative chromosome painting in Spizaetus tyrannus and Gallus gallus with the use of macro- and microchromosome probes

PLOS ONE, 2021

Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes... more Although most birds show karyotypes with diploid number (2n) around 80, with few macrochromosomes and many microchromosomes pairs, some groups, such as the Accipitriformes, are characterized by a large karyotypic reorganization, which resulted in complements with low diploid numbers, and a smaller number of microchromosomal pairs when compared to other birds. Among Accipitriformes, the Accipitridae family is the most diverse and includes, among other subfamilies, the subfamily Aquilinae, composed of medium to large sized species. The Black-Hawk-Eagle (Spizaetus tyrannus-STY), found in South America, is a member of this subfamily. Available chromosome data for this species includes only conventional staining. Hence, in order to provide additional information on karyotype evolution process within this group, we performed comparative chromosome painting between S. tyrannus and Gallus gallus (GGA). Our results revealed that at least 29 fission-fusion events occurred in the STY karyotype...

Research paper thumbnail of Revising the Chromosome-Specific Probes of White Hawk (Leucopternis albicollis)

Proceedings, 2020

Leucopternis albicollis is a diurnal bird of prey with extensive karyotype reorganization. Chromo... more Leucopternis albicollis is a diurnal bird of prey with extensive karyotype reorganization. Chromosome-specific probes from this species have been used successfully to detect intrachromosomal rearrangements in different species of bird since 2010. However, some gaps were detected in this first set of probes. Here, we have obtained a new set of whole chromosome probes in order to improve the previous one; also, we have performed experiments using bacterial artificial chromosome (BAC) from chicken microchromosomes. Our results demonstrated that the microchromosomes were involved in fusion events. In addition, a new nomenclature has been proposed for the new set of probes and some inaccurate data were corrected.

Research paper thumbnail of Validating PGS by probing the karyotypic concordance between ICM and TE

Reproductive Biomedicine Online, 2018

Research paper thumbnail of Sample pooling, a population screening strategy for SARS-CoV2 to prevent future outbreak and mitigate the “second-wave” of infection of the virus

medRxiv, 2020

Problem How do we manage treatment and stabilization in clinical settings and static population c... more Problem How do we manage treatment and stabilization in clinical settings and static population communities like assisted living facility settings of their patient or resident populations during and post the SARS-CoV-2 pandemic? Scope This proposal explores the possible and predicted changes to standard operating procedures to the facility management and associated landscape and focuses on series of deployments, during and post peak SARS-CoV-2 activity, and will outline possible models for the current medical facility model that we operate with. This article primarily focuses on non-emergency facility management. Assumptions and understanding of the field With a reduction in the numbers nationally, patients are highly motivated and likely to seek non-emergency and planned medical procedural treatment as early as possible as social distancing measures are eased and restrictions on non-urgent procedures are lifted. Conclusions and next steps An initial pan-national shutdown and suspen...

Research paper thumbnail of Cattle karyomapping to optimise food production and delivery of superior genetics: the first liveborn calves

Research paper thumbnail of PGS: a four-letter word?

The Biochemist, 2018

Preimplantation genetic screening (PGS) involves the identification of chromosome abnormalities i... more Preimplantation genetic screening (PGS) involves the identification of chromosome abnormalities in IVF embryos (rather than targeting diagnosis to a specified gene). Chiefly employed for couples with advanced maternal age, recurrent miscarriage or recurrent IVF failure, it aims to improve IVF success, and reduce miscarriage and affected live birth rates. The process involves the sampling of cells by embryo biopsy, cytogenetic diagnosis, then selective transfer of an apparently chromosomally normal embryo in the hope of establishing a pregnancy. Although PGS is the most common variant of PGD (preimplantation genetic diagnosis), accounting for 80% of cases it has, from the outset, been one of the most controversial areas of reproductive medicine. The subject of intense debate, it attracts opinions ranging from recommendations that it should be applied in all IVF cases, through to the suggestion it should be discontinued completely. What do you think? Should it continue or not?

Research paper thumbnail of Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

Diversity, 2018

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, ... more Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate an...

Research paper thumbnail of Reporting of Mosaics as High-level and Low level mosaics makes more number of embryos available as alternatives for transfer when no euploid embryos are available

Reproductive BioMedicine Online, 2019

Introduction It is relatively common for human preimplantation embryos produced during the course... more Introduction It is relatively common for human preimplantation embryos produced during the course of IVF treatments to contain two or more cytogenetically distinct cell lines. This phenomenon, known as chromosomal mosaicism, can result in either a mixture of euploid and abnormal cells, or abnormal cells bearing distinct chromosomal gains and losses. NGS allows mosaicism to be detected with much greater sensitivity than earlier preimplantation genetic testing (PGT-A) methods. The application of NGS to trophectoderm biopsies, taken from embryos before transfer to the uterus, has provided insight into the clinical impact of mosaicism. However, because some mosaic embryos are have produced successful pregnancies, it may be appropriate to consider transfer of mosaic embryos in the absence of fully euploid embryos and following patient counseling. Materials and Methods Samples were amplified by SurePlex, sequenced with VeriSeq PGS assay (Illumina) on MiSeq (Illumina) and analyzed with BlueFuse Multi analysis (Illumina). Embryos with at least one fully aneuploid chromosome or one fully aneuploid chromosome and one mosaic chromosome were called aneuploid. Embryos with 3 chromosome abnormalities were designated complex abnormal. Mosaicism was reported when embryos had 20-80% abnormal sequencing profiles. Embryos with low degrees of mosaicism in sequencing profiles were designated as ‘Low –Level Mosaics’. When embryos had high degree of mosaicism, they were reported as ‘High- Level Mosaics’. Design Retrospective analysis of PGS procedures involving TE biopsy and NGS performed by laboratories serving over 250 fertility clinics over three years. A total of 3951 embryos resulting from 952 IVF cycles were analyzed. Results Gross aneuploidy (includes complex abnormals and polyploidies) rates in egg donors (n=402) was 25.62%. Euploid rate in egg donors was 51.00%. 20.90% embryos from egg donors were mosaic, with 11.94% being classified as High-level mosaic and 8.96% being classified as Low-level mosaic. In the non-egg donor group (n=3,545 embryos) aneuploidy (includes complex abnormals and polyploidies) ranged at 44.23%. Euploid rate in non-egg donors was about 36.47%. About 15.94% embryos were mosaic with no trend observed in advanced maternal age and mosaicism. About 8% of all embryos in the non-egg donor group were High-level mosaics while and equal percentage of embryos were Low- level mosaics. A total of 33% cycles (n=317 cycles) resulted in cohorts which had zero euploid embryos. Of these 317 cycles however, 112 cycles (35%), had at least one mosaic embryo to transfer. Of the zero-euploid group a total of 52 cycles (16%) resulted in a Low-level mosaic for patients who otherwise do not have any normal/euploid embryos to transfer. Only 7 cycles from the donor group resulted in cohorts with zero euploid embryos. Conclusion The ability of PGT-A by NGS to delineate between high-level and low-level mosaic embryos allows patients without euploid embryos for transfer the ability to identify mosaic embryos with the greatest likelihood of producing a successful pregnancy. Approximately 8% of all embryos tested by PGT-A are low-level mosaic, with 16% of cycles without identified euploid embryos producing at least one low-level mosaic embryo. The results herein can be used to counsel patients and guide expectations.

Research paper thumbnail of Aneuploidy concordance between trophectoderm and inner cell mass by next-generation sequencingin 100 blastocysts

Reproductive BioMedicine Online, 2019

Introduction A number of clinical trials have reported improved IVF outcomes when embryos are pre... more Introduction A number of clinical trials have reported improved IVF outcomes when embryos are previously vetted for chromosomal aneuploidies, and yet a significant percentage of euploid embryos still fail to implant. Conversely, there is mounting evidence of mosaic embryos leading to pregnancies, and there even exist anecdotal reports of aneuploid embryos resulting in healthy births. Critics of PGT- A point out that a TE biopsy might not correctly represent the entire blastocyst. Genetic discordance between TE and ICM could severely affect the clinical outcomes of PGT-A. Furthermore, a blastocyst classified as aneuploidy might in reality contain a euploid ICM, which could lead to discarding potentially viable embryos in IVFclinics. To date, studies addressing the question of concordance between TE and ICM have relied oncurrently superseded technologies and/or small sample sizes. Here we analyze 100 blastocysts that wereclassified as aneuploid by PGT-A, probing the genetic makup of their paired ICMs using high-resolutionNextGen Sequencing (hr-NGS). Materials & methods We optimized a method to collect ICM biopsies that are free of TE cell contamination, validated by immunofluorescence for lineage markers. Using this technique we isolated ICM biopsies from 100 blastocysts that had previously undergone clinical PGT-A, and had displayed aneuploidy in their TE biopsies (93 whole chromosome aneuploids and 7 segmental aneuploids). All samples were analyzed by hr-NGS, and resulting karyotype profiles of TE and ICM biopsies were compared. We also developed a bioinformatics approach based on SNP analysis and imputation to confirm that the biopsies of blastocysts with TE-ICM discordance indeed stemmed from the same embryo, excluding the possibility of sample mix-up or contamination. Results Comparison of 100 paired TE-ICM karyotypes revealed that a clinical TE biopsy correctly predicts aneuploidy in the ICM in the vast majority of cases. When one or more whole chromosomes were aneuploid in the clinical TE biopsy, the corresponding ICM was aneuploid in 90 out of 93 blastocysts (96.8%). Nonetheless, when the clinical TE biopsy only contained segmental (sub- chromosomal) aneuploidies, the ICM was aneuploid in only 3 out of 7 cases (43%). Combined, and when all types of aneuploidy were considered, an aneuploid TE biopsy correctly predicted aneuploidy in the ICM in 93 outof 100 cases. Of the 7 out of 100 blastocysts that were TE-ICM discordant, the ICM was mosaic in 2 casesand euploid in 5 cases. A second TE biopsy collected from the 7 TE-ICM discordant blastocysts showedconcordance with the original clinical TE biopsy in only 2 out of 7 cases (28%). Conclusions These findings suggest that TE biopsy, in our hands, largely predicts the chromosome constitution of the ICM and this has significant clinical implications. Concomitantly, the results suggest clinical value of reevaluatingblastocysts deemed ‘aneuploid’ in select cases by TE re-biopsy, particularly in instances of segmental aneuploidies.

Research paper thumbnail of Physiological, hyaluronan-selected intracytoplasmic sperm injection for infertility treatment (HABSelect): a parallel, two-group, randomised trial