A Research Roadmap for Next-generation Sequencing Informatics

Overview

Journal Sci Transl Med

Specialties General Medicine
Science

Date 2016 Apr 22

PMID 27099173

Citations 18

Authors

Russ B Altman

Snehit Prabhu

Arend Sidow

Justin M Zook

Rachel Goldfeder

David Litwack

Euan Ashley

George Asimenos

Carlos D Bustamante

Katherine Donigan

Kathleen M Giacomini

Elaine Johansen

Natalia Khuri

Eunice Lee

Xueying Sharon Liang

Marc Salit

Omar Serang

Zivana Tezak

Dennis P Wall

Elizabeth Mansfield

Taha Kass-Hout

Affiliations

Soon will be listed here.

Abstract

Next-generation sequencing technologies are fueling a wave of new diagnostic tests. Progress on a key set of nine research challenge areas will help generate the knowledge required to advance effectively these diagnostics to the clinic.

Citing Articles

Leveraging Systems Immunology to Optimize Diagnosis and Treatment of Inborn Errors of Immunity.

Mauracher A, Henrickson S Front Syst Biol. 2023; 2.

PMID: 37670772 PMC: 10477056. DOI: 10.3389/fsysb.2022.910243.

xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments.

Farek J, Hughes D, Salerno W, Zhu Y, Pisupati A, Mansfield A Gigascience. 2023; 12.

PMID: 36644891 PMC: 9841152. DOI: 10.1093/gigascience/giac125.

Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome.

Reis A, Deveson I, Madala B, Wong T, Barker C, Xu J Genome Biol. 2022; 23(1):19.

PMID: 35022065 PMC: 8753822. DOI: 10.1186/s13059-021-02579-6.

Estimating sequencing error rates using families.

Paskov K, Jung J, Chrisman B, Stockham N, Washington P, Varma M BioData Min. 2021; 14(1):27.

PMID: 33892748 PMC: 8063364. DOI: 10.1186/s13040-021-00259-6.

ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data.

Minoche A, Lundie B, Peters G, Ohnesorg T, Pinese M, Thomas D Genome Med. 2021; 13(1):32.

PMID: 33632298 PMC: 7908648. DOI: 10.1186/s13073-021-00841-x.

References

Dewey F, Chen R, Cordero S, Ormond K, Caleshu C, Karczewski K . Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011; 7(9):e1002280. PMC: 3174201. DOI: 10.1371/journal.pgen.1002280. View

Huang W, Li L, Myers J, Marth G . ART: a next-generation sequencing read simulator. Bioinformatics. 2011; 28(4):593-4. PMC: 3278762. DOI: 10.1093/bioinformatics/btr708. View

Zook J, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W . Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014; 32(3):246-51. DOI: 10.1038/nbt.2835. View

Thatcher S . DNA/RNA preparation for molecular detection. Clin Chem. 2014; 61(1):89-99. DOI: 10.1373/clinchem.2014.221374. View