Exome sequencing of a patient with suspected mitochondrial disease reveals a likely multigenic etiology

BMC Medical Genetics

Volumn 14, Issue 1, 2013, Pages

  Craigen, William J ^a   Graham, Brett H ^a   Wong, Lee Jun ^a   Scaglia, Fernando ^a,b   Lewis, Richard Alan ^a   Bonnen, Penelope E ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b Texas Children's Hospital   (United States)

Author keywords

Diagnostics; Encephalomyopathy; Genocopy; Lowe syndrome; OCRL; SETX

Indexed keywords

ALPHA FETOPROTEIN; CARBOXYLIC ACID; CREATINE KINASE; LACTIC ACID; THYMIDINE;

ADULT; ARTICLE; ATAXIA; CASE REPORT; CATARACT; CATARACT EXTRACTION; CEREBELLUM ATROPHY; CHRONIC PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA; CLINICAL FEATURE; CONGENITAL CATARACT; DENT DISEASE; DISORDERS OF MITOCHONDRIAL FUNCTIONS; ENCEPHALOMYOPATHY; EXOME; FAMILY HISTORY; GENE SEQUENCE; GENETIC SCREENING; HUMAN; HUMAN GENOME; HYPOSPADIAS; INDEL MUTATION; LACTATE BLOOD LEVEL; LEUKOCYTE; LOWE SYNDROME; MALE; MISSENSE MUTATION; MITOCHONDRIAL GENOME; MOLECULAR DIAGNOSIS; MUSCLE BIOPSY; MUSCLE WEAKNESS; NUCLEAR MAGNETIC RESONANCE IMAGING; NUCLEOTIDE SEQUENCE; ONSET AGE; PHYSICAL EXAMINATION; PTOSIS; TREMOR;

ADULT; COMPUTATIONAL BIOLOGY; EXOME; GENETIC DISEASES, X-LINKED; GENETIC LOCI; HOMOZYGOTE; HUMANS; MALE; MITOCHONDRIAL DISEASES; MUTATION, MISSENSE; NEPHROLITHIASIS; OCULOCEREBRORENAL SYNDROME; PEDIGREE; PHENOTYPE; PHOSPHORIC MONOESTER HYDROLASES; RNA HELICASES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPINOCEREBELLAR DEGENERATIONS;

EID: 84881533073     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-14-83     Document Type: Article

References (18)

1. Debray FG, Lambert M, Mitchell GA. Disorders of mitochondrial function. Curr Opin Pediatr 2008, 20(4):471-482. 10.1097/MOP.0b013e328306ebb6, 18622207.
2. Thorburn DR. Mitochondrial disorders: prevalence, myths and advances. J Inherit Metab Dis 2004, 27(3):349-362.
3. Bainbridge MN, Wang M, Wu Y, Newsham I, Muzny DM, Jefferies JL, Albert TJ, Burgess DL, Gibbs RA. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol 2011, 12(7):R68. 10.1186/gb-2011-12-7-r68, 3218830, 21787409.
4. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
5. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43(5):491-498. 10.1038/ng.806, 3083463, 21478889.
6. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 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, 2928508, 20644199.
7. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP. The sequence alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
8. Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res 2001, 11(5):863-874. 10.1101/gr.176601, 311071, 11337480.
9. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010, 7(4):248-249. 10.1038/nmeth0410-248, 2855889, 20354512.
10. Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection 2006, 190-205. Berlin Heidelberg New York: Springer, Proceedings of the 10th International Conference on Research in Computational Molecular Biology RECOMB, 10 3-540-33295-2.
11. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 2011, 32(8):894-899. 10.1002/humu.21517, 3145015,3145015, 21520341.
12. Cooper GM, Stone EA, Asimenos G, Program NCS, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005, 15(7):901-913. 10.1101/gr.3577405, 1172034, 15965027.
13. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 2010, 6(12):e1001025. 10.1371/journal.pcbi.1001025, 2996323, 21152010.
14. Anheim M, Monga B, Fleury M, Charles P, Barbot C, Salih M, Delaunoy JP, Fritsch M, Arning L, Synofzik M, et al. Ataxia with oculomotor apraxia type 2: clinical, biological and genotype/phenotype correlation study of a cohort of 90 patients. Brain 2009, 132(Pt 10):2688-2698.
15. Nussbaum RL, Suchy SF, Lin T. Database of the OCRL1 mutations causing lowe syndrome : , National Human Genome Research Institute, National Institutes of Health, http://www.ncbi.nlm.nih.gov/lovd/home.php?select_db=OCRL.
16. Huang B, He W. Molecular characteristics of inherited congenital cataracts. Eur J Med Genet 2010, 53(6):347-357. 10.1016/j.ejmg.2010.07.001, 20624502.
17. Baranski TJ, Faust PL, Kornfeld S. Generation of a lysosomal enzyme targeting signal in the secretory protein pepsinogen. Cell 1990, 63(2):281-291. 10.1016/0092-8674(90)90161-7, 2170024.
18. Finkel JS, Chinchilla K, Ursic D, Culbertson MR. Sen1p performs two genetically separable functions in transcription and processing of U5 small nuclear RNA in Saccharomyces cerevisiae. Genetics 2010, 184(1):107-118. 10.1534/genetics.109.110031, 2815910, 19884310.