Utilization of genomic sequencing for population screening of immunodeficiencies in the newborn

Genetics in Medicine

Volumn 19, Issue 12, 2017, Pages 1367-1375

  Pavey, Ashleigh R ^a,b,c   Bodian, Dale L ^c   Vilboux, Thierry ^c   Khromykh, Alina ^c   Hauser, Natalie S ^c,d   Huddleston, Kathi ^c   Klein, Elisabeth ^c   Black, Aaron ^c   Kane, Megan S ^c   Iyer, Ramaswamy K ^c   Niederhuber, John E ^c,e   Solomon, Benjamin D ^c,d,f  

^a WALTER REED ARMY MEDICAL CENTER   (United States)

^b UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES   (United States)

^c Inova Translational Medicine Institute   (United States)

^d INOVA CHILDREN S HOSPITAL   (United States)

^e JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f GENEDX   (United States)

Author keywords

Immunodeficiency; Newborn screening; Wholegenome sequencing

Indexed keywords

ARTICLE; CLINICAL FEATURE; COHORT ANALYSIS; CONTROLLED STUDY; ELECTRONIC HEALTH RECORD; FEMALE; GENE FREQUENCY; GENE SEQUENCE; GENETIC SCREENING; GENETIC VARIATION; GENOTYPE; HUMAN; IMMUNE DEFICIENCY; LONGITUDINAL STUDY; LYMPHOCYTOPENIA; MAJOR CLINICAL STUDY; MALE; MOLECULAR DIAGNOSIS; NEWBORN; NEWBORN SCREENING; PATHOGENICITY; PHENOTYPE; SYMPTOMATOLOGY; WHOLE GENOME SEQUENCING; BIOLOGY; GENETICS; INFORMATION PROCESSING; PROCEDURES;

COMPUTATIONAL BIOLOGY; DATA CURATION; FEMALE; GENETIC TESTING; GENOTYPE; HUMANS; IMMUNOLOGIC DEFICIENCY SYNDROMES; INFANT, NEWBORN; MALE; NEONATAL SCREENING; PHENOTYPE; WHOLE GENOME SEQUENCING;

EID: 85034600077     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2017.57     Document Type: Article

References (40)

1. Biesecker L, Green R. Diagnostic clinical genome and exome sequencing. N Engl J Med 2014;370:2418-2425.
2. Solomon B, Lee T, Nguyen A, Wolfsberg T. A 2.5-year snapshot of Mendelian discovery. Mol Genet Genomic Med 2016;4:392-394.
3. Bodian D, Klein E, Iyer R, et al. Utility of whole-genome sequencing for detection of newborn screening disorders in a population cohort of 1, 696 neonates. Genet Med 2016;18:221-230.
4. Stray-Pedersen A, Sorte H, Samarakoon P, et al. Primary immunodeficiency diseases: genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol 2016;S0091-6749:30624-30628.
5. Kwan A, Puck J. History and current status of newborn screening for severe combined immunodeficiency. Semin Perinatol 2015;39:194-205.
6. Notarangelo L. Primary immunodeficiencies. J Allergy Clin Immunol 2010;125:S182-S194.
7. Chan K, Puck JM. Development of population-based newborn screening for severe combined immunodeficiency. J Allergy Clin Immunol 2005;115:391-398.
8. Pai S, Logan BR, Griffith LM, et al. Transplantation outcomes for severe combined immunodeficiency, 2000-2009. N Engl J Med 2014;371: 434-446.
9. Buelow B, Verbsky J, Routes J. Newborn screening for SCID: lessons learned. Expert Rev Hematol 2016;9:579-584.
10. Adams SP, Rashid S, Premachandra T, et al. Screening of neonatal UK dried blood spots using a duplex TREC screening assay. J Clin Immunol 2014;34:323-330.
11. Kanegae M, Barreiros L, Mazzucchelli J, et al. Neonatal screening for severe combined immunodeficiency in Brazil. J Pediatric (Rio J) 2016;92:374-380.
12. Kwan A, Abraham R, Currier R, et al. Newborn screening for severe combined immunodeficiency in 11 screening programs in the United States. JAMA 2014;312:729-738.
13. Raje N, Soden S, Swanson D, Ciaccio C, Kingsmore S, Dinwiddie D. Utility of next generation sequencing in clinical primary immunodeficiencies. Curr Allergy Asthma Rep 2014;14:468.
14. Solomon B, Nguygen A, Bear K, Wolfsberg T. Clinical genomic database. Proc Natl Acad Sci USA 2013;110:9851-9855.
15. Picard C, Al-Herz W, Bousfiha A, et al. Primary immunodeficiency diseases: An update on the classification from the International Union of Immunological Societies Expert Committee for Primary Immunodeficiency 2015. J Clin Immunol 2015;35:696-726.
16. Pruitt K, Brown G, Hiatt S, et al. RefSeq: An update on mammalian reference sequences. Nucleic Acids Res 2014;42:D756-D763.
17. Bailey J, Gu Z, Clark RA, et al. Recent segmental duplications in the human genome. Science 2002;297:1003-1007.
18. Lander E, Linton L, Birren B, et al. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
19. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-1303.
20. Karolchik D, Barber G, Casper J, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res 2014;42:D764-D770.
21. LandrumM, Lee J, Benson M, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 2016;44:D862-D868.
22. Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25:2078-2079.
23. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-Throughput sequencing data. Nucleic Acids Res 2010;38:e164.
24. Auton A, Brooks L, Durbin R, et al. 1000 Genomes Project Consortium: A global reference for human genetic variation. Nature 2015;526:68-74.
25. Lek M, Karczewski K, Minikel E, et al. Analysis of protein-coding genetic variation in 60, 706 humans. Nature 2016;536:285-291.
26. Tan A, Abecasis G, Kang H. Unified representation of genetic variants. Bioinformatics 2015;31:2202-2204.
27. Stenson P, Mort M, Ball E, Shaw K, Phillips A, Cooper D. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet 2014;133:1-9.
28. Glusman G, Severson A, Dhankani V, et al. Identification of copy number variants in whole-genome data using Reference Coverage Profiles. Front Genet. 2015;6:45.
29. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015;17: 405-424.
30. Witzel-Schlomp K, Spath P, Hobart M, et al. The human complement C9 gene: identification of two mutations causing deficiency and revision of the gene structure. J Immunol 1997;158:5043-5049.
31. Hobart M, Fernie B, Würzner R, et al. Difficulties in the ascertainment of C9 deficiency: lessons to be drawn from a compound heterozygote C9-deficient subject. Clin Exp Immunol. 1997;108:500-506.
32. Modell J. 10 warning signs of primary immunodeficiency. Jeffrey Modell Foundation 2012. Available at http://www.info4pi.org/library/educationalmaterials/10-warning-signs. Accessed on 1 February 2016.
33. Casey J, Støve S, McGorrian C, et al. NAA10 mutation causing a novel intellectual disability syndrome with long QT due to N-Terminal acetyltransferase impairment. Sci Rep 2015;5:16022.
34. Saunier C, Stove S, Popp B, et al. Expanding the phenotype associated with NAA10-related N-Terminal acetylation deficiency. Hum Mutat 2016;37:755-764.
35. Shiang R, Ryan S, Zhu Y, Hahn A, O'Connell P, Wasmuth J. Mutations in the [alpha]1 subunit of the inhibitory glycine receptor cause the dominant neurologic disorder, hyperekplexia. Nat Genet 1993;5:351-358.
36. Subbarayan A, Colarusso G, Hughes S, et al. Clinical features that identify children with primary immunodeficiency diseases. Pediatrics 2011;127: 810-816.
37. Boyle J, Buckley R. Population prevalence of diagnosed primary immunodeficiency diseases in the United States. J Clin Immunol 2007;27: 497-502.
38. Lankisch P, Schiffner J, Ghosh S, Barbor F, Borkhardt A, Laws H. The Duesseldorf warning signs for primary immunodeficiency: is it time to change the rules? J Clin Immunol 2015;35:273-279.
39. Beckmann J. Can we afford to sequence every newborn baby's genome? Hum Mutat 2015;36:283-286.
40. Howard H, Knoppers B, Cornel M, et al. Whole-genome sequencing in newborn screening?: A statement on the continued importance of targeted approaches in newborn screening programmes. Eur J Hum Genet 2015;23:1593-1600.