Literature DB >> 28660367

Whole exome sequencing: a state-of-the-art approach for defining (and exploring!) genetic landscapes in pediatric nephrology.

Ashima Gulati1, Stefan Somlo2.   

Abstract

The genesis of whole exome sequencing as a powerful tool for detailing the protein coding sequence of the human genome was conceptualized based on the availability of next-generation sequencing technology and knowledge of the human reference genome. The field of pediatric nephrology enriched with molecularly unsolved phenotypes is allowing the clinical and research application of whole exome sequencing to enable novel gene discovery and provide amendment of phenotypic misclassification. Recent studies in the field have informed us that newer high-throughput sequencing techniques are likely to be of high yield when applied in conjunction with conventional genomic approaches such as linkage analysis and other strategies used to focus subsequent analysis. They have also emphasized the need for the validation of novel genetic findings in large collaborative cohorts and the production of robust corroborative biological data. The well-structured application of comprehensive genomic testing in clinical and research arenas will hopefully continue to advance patient care and precision medicine, but does call for attention to be paid to its integrated challenges.

Entities:  

Keywords:  Clinical genetic sequencing; Genetic kidney diseases; Genetics in nephrology; High-throughput sequencing; Human genetics; Next-generation sequencing

Mesh:

Year:  2017        PMID: 28660367     DOI: 10.1007/s00467-017-3698-0

Source DB:  PubMed          Journal:  Pediatr Nephrol        ISSN: 0931-041X            Impact factor:   3.714


  79 in total

Review 1.  Genetics and pathogenesis of autosomal dominant polycystic kidney disease: 20 years on.

Authors:  Emilie Cornec-Le Gall; Marie-Pierre Audrézet; Yannick Le Meur; Jian-Min Chen; Claude Férec
Journal:  Hum Mutat       Date:  2014-12       Impact factor: 4.878

2.  Mutations of the SLIT2-ROBO2 pathway genes SLIT2 and SRGAP1 confer risk for congenital anomalies of the kidney and urinary tract.

Authors:  Daw-Yang Hwang; Stefan Kohl; Xueping Fan; Asaf Vivante; Stefanie Chan; Gabriel C Dworschak; Julian Schulz; Albertien M van Eerde; Alina C Hilger; Heon Yung Gee; Tracie Pennimpede; Bernhard G Herrmann; Glenn van de Hoek; Kirsten Y Renkema; Christoph Schell; Tobias B Huber; Heiko M Reutter; Neveen A Soliman; Natasa Stajic; Radovan Bogdanovic; Elijah O Kehinde; Richard P Lifton; Velibor Tasic; Weining Lu; Friedhelm Hildebrandt
Journal:  Hum Genet       Date:  2015-05-31       Impact factor: 4.132

3.  Exome sequencing reveals cubilin mutation as a single-gene cause of proteinuria.

Authors:  Bugsu Ovunc; Edgar A Otto; Virginia Vega-Warner; Pawaree Saisawat; Shazia Ashraf; Gokul Ramaswami; Hanan M Fathy; Dominik Schoeb; Gil Chernin; Robert H Lyons; Engin Yilmaz; Friedhelm Hildebrandt
Journal:  J Am Soc Nephrol       Date:  2011-09-08       Impact factor: 10.121

4.  Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform.

Authors:  Rui Chen; Hogune Im; Michael Snyder
Journal:  Cold Spring Harb Protoc       Date:  2015-03-11

5.  Practices and policies of clinical exome sequencing providers: analysis and implications.

Authors:  Seema M Jamal; Joon-Ho Yu; Jessica X Chong; Karin M Dent; Jessie H Conta; Holly K Tabor; Michael J Bamshad
Journal:  Am J Med Genet A       Date:  2013-05       Impact factor: 2.802

6.  ARHGDIA mutations cause nephrotic syndrome via defective RHO GTPase signaling.

Authors:  Heon Yung Gee; Pawaree Saisawat; Shazia Ashraf; Toby W Hurd; Virginia Vega-Warner; Humphrey Fang; Bodo B Beck; Olivier Gribouval; Weibin Zhou; Katrina A Diaz; Sivakumar Natarajan; Roger C Wiggins; Svjetlana Lovric; Gil Chernin; Dominik S Schoeb; Bugsu Ovunc; Yaacov Frishberg; Neveen A Soliman; Hanan M Fathy; Heike Goebel; Julia Hoefele; Lutz T Weber; Jeffrey W Innis; Christian Faul; Zhe Han; Joseph Washburn; Corinne Antignac; Shawn Levy; Edgar A Otto; Friedhelm Hildebrandt
Journal:  J Clin Invest       Date:  2013-07-08       Impact factor: 14.808

7.  Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.

Authors:  Sarah S Kalia; Kathy Adelman; Sherri J Bale; Wendy K Chung; Christine Eng; James P Evans; Gail E Herman; Sophia B Hufnagel; Teri E Klein; Bruce R Korf; Kent D McKelvey; Kelly E Ormond; C Sue Richards; Christopher N Vlangos; Michael Watson; Christa L Martin; David T Miller
Journal:  Genet Med       Date:  2016-11-17       Impact factor: 8.822

8.  FAN1 mutations cause karyomegalic interstitial nephritis, linking chronic kidney failure to defective DNA damage repair.

Authors:  Weibin Zhou; Edgar A Otto; Andrew Cluckey; Rannar Airik; Toby W Hurd; Moumita Chaki; Katrina Diaz; Francis P Lach; Geoffrey R Bennett; Heon Yung Gee; Amiya K Ghosh; Sivakumar Natarajan; Supawat Thongthip; Uma Veturi; Susan J Allen; Sabine Janssen; Gokul Ramaswami; Joanne Dixon; Felix Burkhalter; Martin Spoendlin; Holger Moch; Michael J Mihatsch; Jerome Verine; Richard Reade; Hany Soliman; Michel Godin; Denes Kiss; Guido Monga; Gianna Mazzucco; Kerstin Amann; Ferruh Artunc; Ronald C Newland; Thorsten Wiech; Stefan Zschiedrich; Tobias B Huber; Andreas Friedl; Gisela G Slaats; Jaap A Joles; Roel Goldschmeding; Joseph Washburn; Rachel H Giles; Shawn Levy; Agata Smogorzewska; Friedhelm Hildebrandt
Journal:  Nat Genet       Date:  2012-07-08       Impact factor: 38.330

9.  A global reference for human genetic variation.

Authors:  Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

10.  Exome sequencing from nanogram amounts of starting DNA: comparing three approaches.

Authors:  Vera N Rykalina; Alexey A Shadrin; Vyacheslav S Amstislavskiy; Evgeny I Rogaev; Hans Lehrach; Tatiana A Borodina
Journal:  PLoS One       Date:  2014-07-03       Impact factor: 3.240

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  4 in total

1.  Whole-exome sequencing and variant spectrum in children with suspected inherited renal tubular disorder: the East India Tubulopathy Gene Study.

Authors:  Rajiv Sinha; Subal Pradhan; Sushmita Banerjee; Afsana Jahan; Shakil Akhtar; Amitava Pahari; Sumantra Raut; Prince Parakh; Surupa Basu; Priyanka Srivastava; Snehamayee Nayak; S G Thenral; V Ramprasad; Emma Ashton; Detlef Bockenhauer; Kausik Mandal
Journal:  Pediatr Nephrol       Date:  2022-01-10       Impact factor: 3.651

2.  Establishment of lung cancer patient-derived xenograft models and primary cell lines for lung cancer study.

Authors:  Yanan Jiang; Jimin Zhao; Yi Zhang; Ke Li; Tiepeng Li; Xinhuan Chen; Simin Zhao; Song Zhao; Kangdong Liu; Ziming Dong
Journal:  J Transl Med       Date:  2018-05-22       Impact factor: 5.531

3.  Whole exome sequencing for the identification of CYP3A7 variants associated with tacrolimus concentrations in kidney transplant patients.

Authors:  Minji Sohn; Myeong Gyu Kim; Nayoung Han; In-Wha Kim; Jungsoo Gim; Sang-Il Min; Eun Young Song; Yon Su Kim; Hun Soon Jung; Young Kee Shin; Jongwon Ha; Jung Mi Oh
Journal:  Sci Rep       Date:  2018-12-24       Impact factor: 4.379

4.  Case Report: A Case of β-Ureidopropionase Deficiency Complicated With MELAS Syndrome Caused by UPB1 Variant and Mitochondrial Gene Variant.

Authors:  Jianbo Shu; Xiufang Zhi; Jing Chen; Meifang Lei; Jie Zheng; Wenchao Sheng; Chunhua Zhang; Dong Li; Chunquan Cai
Journal:  Front Pediatr       Date:  2022-02-21       Impact factor: 3.418

  4 in total

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