Literature DB >> 29595809

AUDIOME: a tiered exome sequencing-based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss.

Qiaoning Guan1, Jorune Balciuniene1, Kajia Cao1, Zhiqian Fan1, Sawona Biswas1, Alisha Wilkens1, Daniel J Gallo1, Emma Bedoukian2, Jennifer Tarpinian2, Pushkala Jayaraman1, Mahdi Sarmady1,3, Matthew Dulik1,3, Avni Santani1,3, Nancy Spinner1,3, Ahmad N Abou Tayoun1,3, Ian D Krantz2,4, Laura K Conlin1,3, Minjie Luo5,6.   

Abstract

PURPOSE: Hereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing loss (NSHL) using an exome sequencing (ES) platform and targeted analysis for the curated genes.
METHODS: A tiered strategy was implemented for this test. Tier 1 includes combined Sanger and targeted deletion analyses of the two most common NSHL genes and two mitochondrial genes. Nondiagnostic tier 1 cases are subjected to ES and array followed by targeted analysis of the remaining AUDIOME genes.
RESULTS: ES resulted in good coverage of the selected genes with 98.24% of targeted bases at >15 ×. A fill-in strategy was developed for the poorly covered regions, which generally fell within GC-rich or highly homologous regions. Prospective testing of 33 patients with NSHL revealed a diagnosis in 11 (33%) and a possible diagnosis in 8 cases (24.2%). Among those, 10 individuals had variants in tier 1 genes. The ES data in the remaining nondiagnostic cases are readily available for further analysis.
CONCLUSION: The tiered and ES-based test provides an efficient and cost-effective diagnostic strategy for NSHL, with the potential to reflex to full exome to identify causal changes outside of the AUDIOME test.

Entities:  

Keywords:  exome sequencing; hearing loss; next-generation sequencing panel; reflex; tier

Mesh:

Year:  2018        PMID: 29595809     DOI: 10.1038/gim.2018.48

Source DB:  PubMed          Journal:  Genet Med        ISSN: 1098-3600            Impact factor:   8.822


  12 in total

Review 1.  Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings.

Authors:  Wafaa Abbasi; Courtney E French; Shira Rockowitz; Margaret A Kenna; A Eliot Shearer
Journal:  Hum Genet       Date:  2021-11-22       Impact factor: 4.132

Review 2.  Long-read sequencing for molecular diagnostics in constitutional genetic disorders.

Authors:  Laura K Conlin; Erfan Aref-Eshghi; Deborah A McEldrew; Minjie Luo; Ramakrishnan Rajagopalan
Journal:  Hum Mutat       Date:  2022-09-18       Impact factor: 4.700

3.  Systematic evaluation of gene variants linked to hearing loss based on allele frequency threshold and filtering allele frequency.

Authors:  John Hoon Rim; Joon Suk Lee; Jinsei Jung; Ji Hyun Lee; Seung-Tae Lee; Jong Rak Choi; Jae Young Choi; Min Goo Lee; Heon Yung Gee
Journal:  Sci Rep       Date:  2019-03-14       Impact factor: 4.379

4.  Use of a Dynamic Genetic Testing Approach for Childhood-Onset Epilepsy.

Authors:  Jorune Balciuniene; Elizabeth T DeChene; Gozde Akgumus; Edward J Romasko; Kajia Cao; Holly A Dubbs; Surabhi Mulchandani; Nancy B Spinner; Laura K Conlin; Eric D Marsh; Ethan Goldberg; Ingo Helbig; Mahdi Sarmady; Ahmad Abou Tayoun
Journal:  JAMA Netw Open       Date:  2019-04-05

5.  Increased diagnostic yield by reanalysis of data from a hearing loss gene panel.

Authors:  Yu Sun; Jiale Xiang; Yidong Liu; Sen Chen; Jintao Yu; Jiguang Peng; Zijing Liu; Lisha Chen; Jun Sun; Yun Yang; Yaping Yang; Yulin Zhou; Zhiyu Peng
Journal:  BMC Med Genomics       Date:  2019-05-28       Impact factor: 3.063

6.  A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data.

Authors:  Ramakrishnan Rajagopalan; Jill R Murrell; Minjie Luo; Laura K Conlin
Journal:  Genome Med       Date:  2020-01-30       Impact factor: 11.117

Review 7.  Application of Next Generation Sequencing in Laboratory Medicine.

Authors:  Yiming Zhong; Feng Xu; Jinhua Wu; Jeffrey Schubert; Marilyn M Li
Journal:  Ann Lab Med       Date:  2020-08-25       Impact factor: 3.464

8.  Molecular diagnosis of non-syndromic hearing loss patients using a stepwise approach.

Authors:  Jing Wang; Jiale Xiang; Lisha Chen; Hongyu Luo; Xiuhua Xu; Nan Li; Chunming Cui; Jingjing Xu; Nana Song; Jiguang Peng; Zhiyu Peng
Journal:  Sci Rep       Date:  2021-02-17       Impact factor: 4.379

9.  A multiplex PCR amplicon sequencing assay to screen genetic hearing loss variants in newborns.

Authors:  Haiyan Yang; Hongyu Luo; Guiwei Zhang; Junqing Zhang; Zhiyu Peng; Jiale Xiang
Journal:  BMC Med Genomics       Date:  2021-02-27       Impact factor: 3.063

Review 10.  Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution.

Authors:  Emilie Lalonde; Stefan Rentas; Fumin Lin; Matthew C Dulik; Cara M Skraban; Nancy B Spinner
Journal:  Front Pediatr       Date:  2020-07-08       Impact factor: 3.418

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