Challenges of diagnostic exome sequencing in an inbred founder population

Abstract

Exome sequencing was used as a diagnostic tool in a Roma/Gypsy family with three subjects (one deceased) affected by lissencephaly with cerebellar hypoplasia (LCH), a clinically and genetically heterogeneous diagnostic category. Data analysis identified high levels of unreported inbreeding, with multiple rare/novel “deleterious” variants occurring in the homozygous state in the affected individuals. Step-wise filtering was facilitated by the inclusion of parental samples in the analysis and the availability of ethnically matched control exome data. We identified a novel mutation, p.Asp487Tyr, in the VLDLR gene involved in the Reelin developmental pathway and associated with a rare form of LCH, the Dysequilibrium Syndrome. p.Asp487Tyr is the third reported missense mutation in this gene and the first example of a change affecting directly the functionally crucial β-propeller domain. An unexpected additional finding was a second unique mutation (p.Asn494His) with high scores of predicted pathogenicity in KCNV2, a gene implicated in a rare eye disorder, retinal cone dystrophy type 3B. This result raised diagnostic and counseling challenges that could be resolved through mutation screening of a large panel of healthy population controls. The strategy and findings of this study may inform the search for new disease mutations in the largest European genetic isolate.

Founder p.Arg 446* mutation in the PDHX gene explains over half of cases with congenital lactic acidosis in Roma children

“…We used the SeqCap Roche Human Exome V3 capture system (Roche NimbleGen, Madison, WI, USA) and the HiSeq2000 platform (Illumina, San Diego, CA, USA). Initial data processing was done as described previously [9,10]. We used 6491 markers, extracted from WES data at HapMap Phase II SNP positions [10,11] to estimate inbreeding coefficients [12] and relatedness [13].…”

“…Initial data processing was done as described previously [9,10]. We used 6491 markers, extracted from WES data at HapMap Phase II SNP positions [10,11] to estimate inbreeding coefficients [12] and relatedness [13]. The search for the disease-causing mutation focused on variants with a quality score ≥20 and coverage ≥4×, located outside of segmental duplications and simple repeats.…”

Very mild features of dysequilibrium syndrome associated with a novel VLDLR missense mutation

“…Their truncal ataxia was extremely severe, making ambulation and even stance position nearly impossible. Cognitive impairment was moderate to severe, and speech was markedly dysarthric [14].…”

“…Mutations in the (VLDLR) gene, encoding the very low density lipoprotein receptor, represent the most frequent cause of DES, with 16 mutated families reported so far [4,[8][9][10][11][12][13][14][15][16]. The majority of patients harbour loss-of-function mutations, including large deletions of several exons or of the whole gene, non-sense, frameshift or splice-site mutations.…”

“…The majority of patients harbour loss-of-function mutations, including large deletions of several exons or of the whole gene, non-sense, frameshift or splice-site mutations. Only four missense mutations have been identified, of which two in the homozygous state [13,14] and the other two in compound heterozygosity with frameshift mutations [11,17]. Clinical presentation in patients carrying missense variants did not seem to differ from those harbouring definite loss-of-function mutations, arguing against genotypephenotype correlates in DES.…”