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Diagnostic application of targeted resequencing for familial nonsyndromic hearing loss.

Choi BY, Park G, Gim J, Kim AR, Kim BJ, Kim HS, Park JH, Park T, Oh SH, Han KH, Park WY - PLoS ONE (2013)

Bottom Line: Each proband carried 4.8 variants that were not synonymous and had the occurring frequency of less than three among the 20 probands.These variants were then filtered out with the inheritance pattern of the family, allele frequency in normal hearing 80 control subjects, clinical features.Finally NSHL-causing candidate mutations were identified in 13(65%) of the 20 probands of multiplex families, bringing the total solve rate (or detection rate) in our familial cases to be 78.1% (25/32) Damaging mutations discovered by the targeted resequencing were distributed in nine genes such as WFS1, COCH, EYA4, MYO6, GJB3, COL11A2, OTOF, STRC and MYO3A, most of which were private.

View Article: PubMed Central - PubMed

Affiliation: Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea.

ABSTRACT
Identification of causative genes for hereditary nonsyndromic hearing loss (NSHL) is important to decide treatment modalities and to counsel the patients. Due to the genetic heterogeneity in sensorineural genetic disorders, the high-throughput method can be adapted for the efficient diagnosis. To this end, we designed a new diagnostic pipeline to screen all the reported candidate genes for NSHL. For validation of the diagnostic pipeline, we focused upon familial NSHL cases that are most likely to be genetic, rather than to be infectious or environmental. Among the 32 familial NSHL cases, we were able to make a molecular genetic diagnosis from 12 probands (37.5%) in the first stage by their clinical features, characteristic inheritance pattern and further candidate gene sequencing of GJB2, SLC26A4, POU3F4 or mitochondrial DNA. Next we applied targeted resequencing on 80 NSHL genes in the remaining 20 probands. Each proband carried 4.8 variants that were not synonymous and had the occurring frequency of less than three among the 20 probands. These variants were then filtered out with the inheritance pattern of the family, allele frequency in normal hearing 80 control subjects, clinical features. Finally NSHL-causing candidate mutations were identified in 13(65%) of the 20 probands of multiplex families, bringing the total solve rate (or detection rate) in our familial cases to be 78.1% (25/32) Damaging mutations discovered by the targeted resequencing were distributed in nine genes such as WFS1, COCH, EYA4, MYO6, GJB3, COL11A2, OTOF, STRC and MYO3A, most of which were private. Despite the advent of whole genome and whole exome sequencing, we propose targeted resequencing and filtering strategy as a screening and diagnostic tool at least for familial NSHL to find mutations based upon its efficacy and cost-effectiveness.

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Related in: MedlinePlus

Analysis flow of NSHL-80 targeted resequencing on familial NSHL.Targeted resequencing data from 20 familial NSHL cases were filtered through five steps to select candidate SNVs in NSHL genes.
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pone-0068692-g001: Analysis flow of NSHL-80 targeted resequencing on familial NSHL.Targeted resequencing data from 20 familial NSHL cases were filtered through five steps to select candidate SNVs in NSHL genes.

Mentions: Next, we applied targeted resequencing for 20 probands of the remaining familial NSHL cases including one GJB2 positive multiplex family (SH35) to screen all 80 reported NSHL-related genes (Fig. 1). We have captured 1254 exons of 80 genes (Table S2) spanning 480 kb in 20 probands from multiplex families for targeted exome sequencing. Mean read depth in 20 cases was 218.2±56.1 and 88.9±3.7% of bases was read in more than ×10 coverage (Table S3). About 90% exons in all patients were captured with ≥99% of bases at ≥10 of read depth. Missed or low-coverage exons were shared between samples, though different experimental procedures shared different uncaptured exons (Fig. S2). This ensures that most of captured exons were shared through samples, which does not disturb the following analysis of variant detection. The fraction of well-captured exons was much more than expectation by the model of independent uncaptured exons (Figs. S3 and S4).


Diagnostic application of targeted resequencing for familial nonsyndromic hearing loss.

Choi BY, Park G, Gim J, Kim AR, Kim BJ, Kim HS, Park JH, Park T, Oh SH, Han KH, Park WY - PLoS ONE (2013)

Analysis flow of NSHL-80 targeted resequencing on familial NSHL.Targeted resequencing data from 20 familial NSHL cases were filtered through five steps to select candidate SNVs in NSHL genes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3750053&req=5

pone-0068692-g001: Analysis flow of NSHL-80 targeted resequencing on familial NSHL.Targeted resequencing data from 20 familial NSHL cases were filtered through five steps to select candidate SNVs in NSHL genes.
Mentions: Next, we applied targeted resequencing for 20 probands of the remaining familial NSHL cases including one GJB2 positive multiplex family (SH35) to screen all 80 reported NSHL-related genes (Fig. 1). We have captured 1254 exons of 80 genes (Table S2) spanning 480 kb in 20 probands from multiplex families for targeted exome sequencing. Mean read depth in 20 cases was 218.2±56.1 and 88.9±3.7% of bases was read in more than ×10 coverage (Table S3). About 90% exons in all patients were captured with ≥99% of bases at ≥10 of read depth. Missed or low-coverage exons were shared between samples, though different experimental procedures shared different uncaptured exons (Fig. S2). This ensures that most of captured exons were shared through samples, which does not disturb the following analysis of variant detection. The fraction of well-captured exons was much more than expectation by the model of independent uncaptured exons (Figs. S3 and S4).

Bottom Line: Each proband carried 4.8 variants that were not synonymous and had the occurring frequency of less than three among the 20 probands.These variants were then filtered out with the inheritance pattern of the family, allele frequency in normal hearing 80 control subjects, clinical features.Finally NSHL-causing candidate mutations were identified in 13(65%) of the 20 probands of multiplex families, bringing the total solve rate (or detection rate) in our familial cases to be 78.1% (25/32) Damaging mutations discovered by the targeted resequencing were distributed in nine genes such as WFS1, COCH, EYA4, MYO6, GJB3, COL11A2, OTOF, STRC and MYO3A, most of which were private.

View Article: PubMed Central - PubMed

Affiliation: Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, Korea.

ABSTRACT
Identification of causative genes for hereditary nonsyndromic hearing loss (NSHL) is important to decide treatment modalities and to counsel the patients. Due to the genetic heterogeneity in sensorineural genetic disorders, the high-throughput method can be adapted for the efficient diagnosis. To this end, we designed a new diagnostic pipeline to screen all the reported candidate genes for NSHL. For validation of the diagnostic pipeline, we focused upon familial NSHL cases that are most likely to be genetic, rather than to be infectious or environmental. Among the 32 familial NSHL cases, we were able to make a molecular genetic diagnosis from 12 probands (37.5%) in the first stage by their clinical features, characteristic inheritance pattern and further candidate gene sequencing of GJB2, SLC26A4, POU3F4 or mitochondrial DNA. Next we applied targeted resequencing on 80 NSHL genes in the remaining 20 probands. Each proband carried 4.8 variants that were not synonymous and had the occurring frequency of less than three among the 20 probands. These variants were then filtered out with the inheritance pattern of the family, allele frequency in normal hearing 80 control subjects, clinical features. Finally NSHL-causing candidate mutations were identified in 13(65%) of the 20 probands of multiplex families, bringing the total solve rate (or detection rate) in our familial cases to be 78.1% (25/32) Damaging mutations discovered by the targeted resequencing were distributed in nine genes such as WFS1, COCH, EYA4, MYO6, GJB3, COL11A2, OTOF, STRC and MYO3A, most of which were private. Despite the advent of whole genome and whole exome sequencing, we propose targeted resequencing and filtering strategy as a screening and diagnostic tool at least for familial NSHL to find mutations based upon its efficacy and cost-effectiveness.

Show MeSH
Related in: MedlinePlus