Genetic diagnosis in consanguineous families with kidney disease by homozygosity mapping coupled with whole-exome sequencing - PubMed (original) (raw)

doi: 10.1053/j.ajkd.2011.01.025. Epub 2011 Jun 12.

Giulio Genovese, Hamad Al-Mojalli, Saleh Al-Othman, Hadeel Al-Manea, Mohammed Al-Suleiman, Mohammed Al-Jondubi, Nourah Atallah, Maha Al-Rodayyan, Astrid Weins, Martin R Pollak, Chaker N Adra

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Genetic diagnosis in consanguineous families with kidney disease by homozygosity mapping coupled with whole-exome sequencing

Khaldoun I Al-Romaih et al. Am J Kidney Dis. 2011 Aug.

Abstract

Background: Accurate diagnosis of the primary cause of an individual's kidney disease can be essential for proper management. Some kidney diseases have overlapping histopathologic features despite being caused by defects in different genes. In this report, we describe 2 consanguineous Saudi Arabian families in which individuals presented with kidney failure and mixed clinical and histologic features initially believed to be consistent with focal segmental glomerulosclerosis.

Study design: Case series.

Setting & participants: We studied members of 2 apparently unrelated families from Saudi Arabia with kidney disease.

Measurements: Whole-genome single-nucleotide polymorphism analysis followed by targeted isolation and sequencing of exons using genomic DNA samples from affected members of these families, followed by additional focused genotyping and sequence analysis.

Results: The 2 apparently unrelated families shared a region of homozygosity on chromosome 2q13. Exome sequence from affected individuals lacked sequence reads from the NPHP1 gene, which is located within this homozygous region. Additional polymerase chain reaction-based genotyping confirmed that affected individuals had NPHP1 deletions, rather than defects in a known focal segmental glomerulosclerosis-associated gene.

Limitations: The methods used here may not result in a clear genetic diagnosis in many cases of apparent familial kidney disease.

Conclusions: This analysis shows the power of new high-throughput genotyping and sequencing technologies to aid in the rapid genetic diagnosis of individuals with an inherited form of kidney disease. We believe it is likely that such tools may become useful clinical genetic tools and alter the manner in which diagnoses are made in nephrology.

Copyright © 2011 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

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Figures

Figure 1

Figure 1

Homozygosity Mapping in Two Consanguineous Families. Pedigrees for a) family 12 (FAM012) and b) family 1 (FAM001) are shown. Squares indicate males and circles females. Pedigree identifier is shown in the bottom of the figure. Arrow heads point to affected subjects who share the homozygous runs that are indicated in red bar on the chromosome view in the right side for each pedigree.

Figure 2

Figure 2

Kidney biopsy findings in an affected member of FAM012 (KFH-46). a) Masson’s trichrome stain representation of a glomerulus showing glomerular tuft segmental sclerosis in the superior half; segments in the inferior half display mesangium and capillary walls and lumens with conserved architecture. b) Direct immunofluorescence showing focal staining for C3 and IgM in the sclerosed glomerular segments. c) and d) Electron micrographs revealing areas of extensive foot process effacement (red arrowheads) and glomerular basement membrane wrinkling, changes indicating FSGS.

Figure 3

Figure 3

Homozygous run shared in FAM012 and FAM001. The homozygous run localizes between rs6754115 (genomic position 109,328,776) and rs17464100 (genomic position 111,284,252) and the critical homozygous interval is ~ 2 Mb.

Figure 4

Figure 4

Exome capture and sequence data from the NPHP1/MALL locus. In RKH-5 (affected), there is zero sequencing coverage inside the deletion, while in KFH-41 (unaffected) there was an average coverage of 74× (black arrowheads). Both RKH-5 and KFH-41 had sequencing coverage in the region outside the deletion (red arrowheads). This figure was generated using Integrated Genomic View:

http://www.broadinstitute.gov/igv/

.

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