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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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Interpretation of targeted resequencing in 20 probands.(A) An average number of candidate SNVs with standard errors were shown at five filtering steps. (B) The relationship between the numbers of candidate SNVs and read depth were plotted in 20 probands. (C) Candidate SNV-found patient group (Found) was compared with patient group without candidate SNV (Not-found) in the number of candidate variants, read depth and called SNVs.
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pone-0068692-g003: Interpretation of targeted resequencing in 20 probands.(A) An average number of candidate SNVs with standard errors were shown at five filtering steps. (B) The relationship between the numbers of candidate SNVs and read depth were plotted in 20 probands. (C) Candidate SNV-found patient group (Found) was compared with patient group without candidate SNV (Not-found) in the number of candidate variants, read depth and called SNVs.

Mentions: Among 32 familial NSHL cases, we could detect mutations in 25 probands (79.1%) by Sanger and targeted exome sequencing in total. Breaking into the results depending upon the inheritance pattern, we were able to make a molecular genetic diagnosis from 9 (69.2%) of 13 autosomal dominant families on. seven genes such as WFS1, COCH, EYA4, MYO6, GJB3, COL11A2 and OTOR. Molecular genetic diagnosis was possible in 9 (75.0%) of 12 recessive families. The four probably or possibly damaging mutations that we found were in SLC26A4, GJB2, MYO3A, OTOF, and STRC. We also found one case with MRNR1 mutation with maternal inheritance, and five cases of POU3F4 mutation with X-linked inheritance. However, we could not detect candidate mutations in seven probands, in which the number of variants from basic filtering was not correlated with read depth in 20 probands (Fig. 3A). The number of called variants, sequencing depth and mean coverage was not different from those with candidate mutations detected (Figs. 3B and 3C).


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)

Interpretation of targeted resequencing in 20 probands.(A) An average number of candidate SNVs with standard errors were shown at five filtering steps. (B) The relationship between the numbers of candidate SNVs and read depth were plotted in 20 probands. (C) Candidate SNV-found patient group (Found) was compared with patient group without candidate SNV (Not-found) in the number of candidate variants, read depth and called SNVs.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0068692-g003: Interpretation of targeted resequencing in 20 probands.(A) An average number of candidate SNVs with standard errors were shown at five filtering steps. (B) The relationship between the numbers of candidate SNVs and read depth were plotted in 20 probands. (C) Candidate SNV-found patient group (Found) was compared with patient group without candidate SNV (Not-found) in the number of candidate variants, read depth and called SNVs.
Mentions: Among 32 familial NSHL cases, we could detect mutations in 25 probands (79.1%) by Sanger and targeted exome sequencing in total. Breaking into the results depending upon the inheritance pattern, we were able to make a molecular genetic diagnosis from 9 (69.2%) of 13 autosomal dominant families on. seven genes such as WFS1, COCH, EYA4, MYO6, GJB3, COL11A2 and OTOR. Molecular genetic diagnosis was possible in 9 (75.0%) of 12 recessive families. The four probably or possibly damaging mutations that we found were in SLC26A4, GJB2, MYO3A, OTOF, and STRC. We also found one case with MRNR1 mutation with maternal inheritance, and five cases of POU3F4 mutation with X-linked inheritance. However, we could not detect candidate mutations in seven probands, in which the number of variants from basic filtering was not correlated with read depth in 20 probands (Fig. 3A). The number of called variants, sequencing depth and mean coverage was not different from those with candidate mutations detected (Figs. 3B and 3C).

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