Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Stranneheim, Henrik ^a,b   Engvall, Martin ^a,b   Naess, Karin ^b,c   Lesko, Nicole ^b,c   Larsson, Pontus ^d   Dahlberg, Mats ^d   Andeer, Robin ^a   Wredenberg, Anna ^b,c   Freyer, Chris ^b,c   Barbaro, Michela ^a,b   Bruhn, Helene ^b,c   Emahazion, Tesfail ^a,b   Magnusson, Måns ^a   Wibom, Rolf ^b,c   Zetterström, Rolf H ^a,b   Wirta, Valtteri ^e   von Döbeln, Ulrika ^b,c   Wedell, Anna ^a,b  

^a SCIENCE FOR LIFE LABORATORY   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

^d STOCKHOLM UNIVERSITY   (Sweden)

^e ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

Bioinformatics; Clinical diagnosis; Inborn errors of metabolism; Mendelian disease; MPS; WGS

Indexed keywords

ARTICLE; AUTOMATION; CASE REPORT; CHILD; DATA BASE; DATA PROCESSING; FOLLOW UP; GENE MUTATION; GENETIC COUNSELING; GENETIC PROCEDURES; HUMAN; INBORN ERROR OF METABOLISM; INFORMED CONSENT; METHODOLOGY; OUTCOME ASSESSMENT; PRACTICE GUIDELINE; PREDICTION; RETROSPECTIVE STUDY; WHOLE GENOME SEQUENCING; BIOLOGY; DNA SEQUENCE; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; METABOLISM, INBORN ERRORS;

PYRUVATE DEHYDROGENASE; PYRUVATE DEHYDROGENASE E1ALPHA SUBUNIT;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METABOLISM, INBORN ERRORS; PYRUVATE DEHYDROGENASE (LIPOAMIDE); SEQUENCE ANALYSIS, DNA;

EID: 84924290563     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-1090     Document Type: Article

References (20)

1. Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM: Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013,369(16):1502-1511. 10.1056/NEJMoa1306555
2. American Society of Human Genetics Board of Directors: Points to consider: ethical, legal, and psychosocial implications of genetic testing in children and adolescents. Am J Hum Genet 1995,57(5):1233-1241.
3. Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E: ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013,15(9):733-747. 10.1038/gim.2013.92
4. van El CG, Cornel MC, Borry P, Hastings RJ, Fellmann F, Hodgson SV, Howard HC, Cambon-Thomsen A, Knoppers BM, Meijers-Heijboer H, Scheffer H, Tranebjaerg L, Dondorp W, de Wert GM: Whole-genome sequencing in health care: recommendations of the European Society of Human Genetics. Eur J Hum Genet 2013,21(6):580-584.
5. Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, Andraws N, Patterson ML, Krivohlavek LA, Fellis J, Humphray S, Saffrey P, Kingsbury Z, Weir JC, Betley J, Grocock RJ, Margulies EH, Farrow EG, Artman M, Safina NP, Petrikin JE, Hall KP, Kingsmore SF: Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med 2012,4(154):154ra135.
6. Mutation Identification Pipeline [ https://github.com/henrikstranneheim/MIP ]
7. Kraus JP, Spector E, Venezia S, Estes P, Chiang PW, Creadon-Swindell G, Mullerleile S, de Silva L, Barth M, Walter M, Walter K, Meissner T, Lindner M, Ensenauer R, Santer R, Bodamer OA, Baumgartner MR, Brunner-Krainz M, Karall D, Haase C, Knerr I, Marquardt T, Hennermann JB, Steinfeld R, Beblo S, Koch HG, Konstantopoulou V, Scholl-Burgi S, van Teeffelen-Heithoff A, Suormala T, et al.: Mutation analysis in 54 propionic acidemia patients. J Inherit Metab Dis 2012,35(1):51-63. 10.1007/s10545-011-9399-0
8. Dahl HH, Hansen LL, Brown RM, Danks DM, Rogers JG, Brown GK: X-linked pyruvate dehydrogenase E1 alpha subunit deficiency in heterozygous females: variable manifestation of the same mutation. J Inherit Metab Dis 1992,15(6):835-847. 10.1007/BF01800219
9. Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, et al.: The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009,19(7):1316-1323. 10.1101/gr.080531.108
10. Ghosh S, Bee G, Reddy M, Pickle L, Dudas M, Del Mistro G, Sedova M, Reed B, Bennett R, and the Ion Torrent R&D Team: Semiconductor Sequencing of Human Exomes on the Ion Proton System. J Biomol Tech 2013,24(Suppl):S44.
11. Chanjo [ https://github.com/robinandeer/chanjo ]
12. Stenson PD, Ball EV, Howells K, Phillips AD, Mort M, Cooper DN: The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. Hum Genomics 2009,4(2):69-72. 10.1186/1479-7364-4-2-69
13. pulse_conversion.py [ https://github.com/SciLifeLab/scilifelab/blob/master/scripts/pulse_conversion.py ]
14. Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009,25(14):1754-1760. 10.1093/bioinformatics/btp324
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009,25(16):2078-2079. 10.1093/bioinformatics/btp352
16. Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010,26(6):841-842. 10.1093/bioinformatics/btq033
17. PicardTools [ http://broadinstitute.github.io/picard/ ]
18. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011,43(5):491-498. 10.1038/ng.806
19. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010,20(9):1297-1303. 10.1101/gr.107524.110
20. Wang K, Li M, Hakonarson H: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010,38(16):e164. 10.1093/nar/gkq603