NISC - NIH Intramural Sequencing Center Publications

NISC Publications

Summers AC, Snow J, Wiggs E, Liu AG, Toro C, Poretti A, Zein WM, Brooks BP, Parisi MA, Inati S, Doherty D, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Vilboux T, Gahl WA, Gunay-Aygun M. Neuropsychological phenotypes of 76 individuals with Joubert syndrome evaluated at a single center. Am J Med Genet A. 2017 May 12. doi: 10.1002/ajmg.a.38272. 28497568
Le Gallo M, Rudd ML, Urick ME, Hansen NF, Zhang S, NISC Comparative Sequencing Program, Lozy F, Sgroi DC, Vidal Bel A, Matias-Guiu X, Broaddus RR, Lu KH, Levine DA, Mutch DG, Goodfellow PJ, Salvesen HB, Mullikin JC, Bell DW. Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing. Cancer. 2017 May 9. doi: 10.1002/cncr.30745. 2848515
Shahrour MA, Staretz-Chacham O, Dayan D, Stephen J, Weech A, Damseh N, Pri Chen H, Edvardson S, Mazaheri S, Saada A, NISC Intramural Sequencing, Hershkovitz E, Shaag A, Huizing M, Abu-Libdeh B, Gahl WA, Azem A, Anikster Y, Vilboux T, Elpeleg O, Malicdan MC. Mitochondrial epileptic encephalopathy, 3-methylglutaconic aciduria and variable complex V deficiency associated with TIMM50 mutations. Clin Genet. 2017 May;91(5):690-696. doi: 10.1111/cge.12855. 27573165
Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thöny B, Shen N, Guarani V, Meissner T, Mayatepek E, Trefz FK, Marek-Yagel D, Martinez A, Huttlin EL, Paulo JA, Berutti R, Benoist JF, Imbard A, Dorboz I, Heimer G, Landau Y, Ziv-Strasser L, Malicdan MC, Gemperle-Britschgi C, Cremer K, Engels H, Meili D, Keller I, Bruggmann R, Strom TM, Meitinger T, Mullikin JC, Schwartz G, Ben-Zeev B, Gahl WA, Harper JW, Blau N, Hoffmann GF, Prokisch H, Opladen T, Schiff M. Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. Am J Hum Genet. 2017 Feb 2;100(2):257-266. doi: 10.1016/j.ajhg.2017.01.002. 28132689
Bryan MM, Tolman NJ, Simon KL, Huizing M, Hufnagel RB, Brooks BP, Speransky V, Mullikin JC, Gahl WA, Malicdan MC, Gochuico BR. Clinical and molecular phenotyping of a child with Hermansky-Pudlak syndrome-7, an uncommon genetic type of HPS. Mol Genet Metab. 2017 Feb 27. pii: S1096-7192(16)30413-9. doi: 10.1016/j.ymgme.2017.02.007. 28259707
Stephen J, Vilboux T, Mian L, Kuptanon C, Sinclair CM, Yildirimli D, Maynard DM, Bryant J, Fischer R, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Huizing M, Gahl WA, Malicdan MC, Gunay-Aygun M. Mutations in KIAA0753 cause Joubert syndrome associated with growth hormone deficiency. Hum Genet. 2017 Feb 20. doi: 10.1007/s00439-017-1765-z. 28220259
Berger SI, Ciccone C, Simon KL, Malicdan MC, Vilboux T, Billington C, Fischer R, Introne WJ, Gropman A, Blancato JK, Mullikin JC, NISC Comparative Sequencing Program, Gahl WA, Huizing M, Smith AC. Exome analysis of Smith-Magenis-like syndrome cohort identifies de novo likely pathogenic variants. Hum Genet. 2017 Feb 17. doi: 10.1007/s00439-017-1767-x. 28213671
Varshney A, Scott LJ, Welch RP, Erdos MR, Chines PS, Narisu N, Albanus RD, Orchard P, Wolford BN, Kursawe R, Vadlamudi S, Cannon ME, Didion JP, Hensley J, Kirilusha A, NISC Comparative Sequencing Program, Bonnycastle LL, Taylor DL, Watanabe R, Mohlke KL, Boehnke M, Collins FS, Parker SC, Stitzel ML. Genetic regulatory signatures underlying islet gene expression and type 2 diabetes. Proc Natl Acad Sci U S A. 2017 Feb 13. pii: 201621192. doi: 10.1073/pnas.1621192114. 28193859
Dewan R, Pemov A, Dutra AS, Pak ED, Edwards NA, Ray-Chaudhury A, Hansen NF, Chandrasekharappa SC, Mullikin JC, Asthagiri AR, NISC Comparative Sequencing Program, Heiss JD, Stewart DR, Germanwala AV. First insight into the somatic mutation burden of neurofibromatosis type 2-associated grade I and grade II meningiomas: a case report comprehensive genomic study of two cranial meningiomas with vastly different clinical presentation. BMC Cancer. 2017 Feb 13;17(1):127. doi: 10.1186/s12885-017-3127-6. 28193203
Kwon EM, Connelly JP, Hansen NF, Donovan FX, Winkler T, Davis BW, Alkadi H, Chandrasekharappa SC, Dunbar CE, Mullikin JC, Liu P. iPSCs and fibroblast subclones from the same fibroblast population contain comparable levels of sequence variations. Proc Natl Acad Sci U S A. 2017 Feb 6. pii: 201616035. doi: 10.1073/pnas.1616035114. 28167771
Loftus SK, Baxter LL, Cronin JC, Fufa TD, NISC Comparative Sequencing Program, Pavan WJ. Hypoxia-induced HIF1α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis. Pigment Cell Melanoma Res. 2017 Feb 6. doi: 10.1111/pcmr.12579. 28168807
Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thöny B, Shen N, Guarani V, Meissner T, Mayatepek E, Trefz FK, Marek-Yagel D, Martinez A, Huttlin EL, Paulo JA, Berutti R, Benoist JF, Imbard A, Dorboz I, Heimer G, Landau Y, Ziv-Strasser L, Malicdan MC, Gemperle-Britschgi C, Cremer K, Engels H, Meili D, Keller I, Bruggmann R, Strom TM, Meitinger T, Mullikin JC, Schwartz G, Ben-Zeev B, Gahl WA, Harper JW, Blau N, Hoffmann GF, Prokisch H, Opladen T, Schiff M. Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. Am J Hum Genet. 2017 Jan 26. pii: S0002-9297(17)30002-2. doi: 10.1016/j.ajhg.2017.01.002. 28132689
Vilboux T, Doherty DA, Glass IA, Parisi MA, Phelps IG, Cullinane AR, Zein W, Brooks BP, Heller T, Soldatos A, Oden NL, Yildirimli D, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Malicdan MC, Gahl WA, Gunay-Aygun M. Molecular genetic findings and clinical correlations in 100 patients with Joubert syndrome and related disorders prospectively evaluated at a single center. Genet Med. 2017 Jan 26. doi: 10.1038/gim.2016.204. 28125082
Kambouris M, Thevenon J, Soldatos A, Cox A, Stephen J, Ben-Omran T, Al-Sarraj Y, Boulos H, Bone W, Mullikin JC, NISC Comparative Sequencing Program, Masurel-Paulet A, St-Onge J, Dufford Y, Chantegret C, Thauvin-Robinet C, Al-Alami J, Faivre L, Riviere JB, Gahl WA, Bassuk AG, Malicdan MC, El-Shanti H. Biallelic SCN10A mutations in neuromuscular disease and epileptic encephalopathy. Ann Clin Transl Neurol. 2016 Dec 20;4(1):26-35. doi: 10.1002/acn3.372. 28078312
Poretti A, Snow J, Summers AC, Tekes A, Huisman TA, Aygun N, Carson KA, Doherty D, Parisi MA, Toro C, Yildirimli D, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program , Cullinane AR, Vilboux T, Gahl WA, Gunay-Aygun M. Joubert syndrome: neuroimaging findings in 110 patients in correlation with cognitive function and genetic cause. J Med Genet. 2017 Jan 13. pii: jmedgenet-2016-104425. doi: 10.1136/jmedgenet-2016-104425. 28087721
Pemov A, Li H, Patidar R, Hansen NF, Sindiri S, Hartley SW, Wei JS, Elkahloun A, Chandrasekharappa SC, NISC Comparative Sequencing Program, Boland JF, Bass S, NCI DCEG Cancer Genomics Research Laboratory, Mullikin JC, Khan J, Widemann BC, Wallace MR, Stewart DR. The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas. Oncogene. 2017 Jan 9. doi: 10.1038/onc.2016.464. 28068329
Vilboux T, Malicdan MC, Roney JC, Cullinane AR, Stephen J, Yildirimli D, Bryant J, Fischer R, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Steinbach PJ, Gahl WA, Gunay-Aygun M. CELSR2, encoding a planar cell polarity protein, is a putative gene in Joubert syndrome with cortical heterotopia, microophthalmia, and growth hormone deficiency. Am J Med Genet A. 2017 Jan 4. doi: 10.1002/ajmg.a.38005. 28052552
Falik Zaccai TC, Savitzki D, Zivony-Elboum Y, Vilboux T, Fitts EC, Shoval Y, Kalfon L, Samra N, Keren Z, Gross B, Chasnyk N, Straussberg R, Mullikin JC, Teer JK, Geiger D, Kornitzer D, Bitterman-Deutsch O, Samson AO, Wakamiya M, Peterson JW, Kirtley ML, Pinchuk IV, Baze WB, Gahl WA, Kleta R, Anikster Y, Chopra AK. Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy. Brain. 2016 Dec 21. pii: aww295. doi: 10.1093/brain/aww295. 28007986
Gopinath C, Law WD, Rodríguez-Molina JF, Prasad AB, Song L, Crawford GE, Mullikin JC, Svaren J, Antonellis A. Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation. BMC Genomics. 2016 Nov 7;17(1):887. doi: 10.1186/s12864-016-3167-3 27821050
Winter JM, Gildea DE, Andreas JP, Gatti DM, Williams KA, Lee M, Hu Y, Zhang S, NISC Comparative Sequencing Program, Mullikin JC, Wolfsberg TG, McDonnell SK, Fogarty ZC, Larson MC, French AJ, Schaid DJ, Thibodeau SN, Churchill GA, Crawford NP. Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer. Cell Syst. 2016 Nov 25. pii: S2405-4712(16)30361-1. doi: 10.1016/j.cels.2016.10.018. 27916600
O'Brien KJ, Lozier J, Cullinane AR, Osorio B, Nghiem K, Speransky V, Zein WM, Mullikin JC, Neff AT, Simon KL, Malicdan MC, Gahl WA, Young LR, Gochuico BR. Identification of a novel mutation in HPS6 in a patient with hemophilia B and oculocutaneous albinism. Mol Genet Metab. 2016 Nov;119(3):284-287. doi: 10.1016/j.ymgme.2016.08.009. 27641950
Hartley SW, Mullikin JC, Klein DC, Park M, NISC Comparative Sequencing Program, Coon SL. Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation. PLoS One. 2016 Sep 29;11(9):e0163590. doi: 10.1371/journal.pone.0163590. 27684375
Török A, Schiffer PH, Schnitzler CE, Ford K, Mullikin JC, Baxevanis AD, Bacic A, Frank U, Gornik SG. The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA. Epigenetics Chromatin. 2016 Sep 6;9(1):36. doi: 10.1186/s13072-016-0085-1. 27602058
Ng D, Hong CS, Singh LN, Johnston JJ, Mullikin JC, Biesecker LG. Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening. Genet Med. 2016 Aug 18. doi: 10.1038/gim.2016.105. 27537706
Hong CS, Singh LN, Mullikin JC, Biesecker LG. Assessing the reproducibility of exome copy number variations predictions. Genome Med. 2016 Aug 8;8(1):82. doi: 10.1186/s13073-016-0336-6. 27503473
Conlan S, Lau AF, NISC Comparative Sequencing Program, Palmore TN, Frank KM, Segre JA. Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid. Genome Announc. 2016 Jul 14;4(4). pii: e00664-16. doi: 10.1128/genomeA.00664-16. 27417839
Margolin G, Petrykowska HM, Jameel N, Bell DW, Young AC, Elnitski L. Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development. J Mol Diagn. 2016 Mar;18(2):283-98. doi: 10.1016/j.jmoldx.2015.11.004. Epub 2016 Feb 5. 26857064
Zhou Q, Yu X, Demirkaya E, Deuitch N, Stone D, Tsai WL, Kuehn HS, Wang H, Yang D, Park YH, Ombrello AK, Blake M, Romeo T, Remmers EF, Chae JJ, Mullikin JC, Güzel F, Milner JD, Boehm M, Rosenzweig SD, Gadina M, Welch SB, Özen S, Topaloglu R, Abinun M, Kastner DL, Aksentijevich I. Biallelic hypomorphic mutations in a linear deubiquitinase define otulipenia, an early-onset autoinflammatory disease. Proc Natl Acad Sci U S A. 2016 Aug 24. pii: 201612594. 27559085
Jo JH, Deming C, Kennedy EA, Conlan S, Polley EC, Ng WL; NISC Comparative Sequencing Program, Segre JA, Kong HH. Diverse human skin fungal communities in children converge in adulthood. J Invest Dermatol. 2016 Jul 28. pii: S0022-202X(16)32231-X. doi: 10.1016/j.jid.2016.05.130 27476723
Joyce MG, Wheatley AK, Thomas PV, Chuang GY, Soto C, Bailer RT, Druz A, Georgiev IS, Gillespie RA, Kanekiyo M, Kong WP, Leung K, Narpala SN, Prabhakaran MS, Yang ES, Zhang B, Zhang Y, Asokan M, Boyington JC, Bylund T, Darko S, Lees CR, Ransier A, Shen CH, Wang L, Whittle JR, Wu X, Yassine HM, Santos C, Matsuoka Y, Tsybovsky Y, Baxa U, NISC Comparative Sequencing Program, Mullikin JC, Subbarao K, Douek DC, Graham BS, Koup RA, Ledgerwood JE, Roederer M, Shapiro L, Kwong PD, Mascola JR, McDermott AB. Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses. Cell. 2016 Jul 28;166(3):609-23. doi: 10.1016/j.cell.2016.06.043. Epub 2016 Jul 21. 27453470
Maglic D, Stephen J, Malicdan MC, Guo J, Fischer R, Konzman D, NISC Comparative Sequencing Program, Mullikin JC, Gahl WA, Vilboux T, Gunay-Aygun M. TMEM231 Gene Conversion Associated with Joubert and Meckel-Gruber Syndromes in the Same Family. Hum Mutat. 2016 Jul 23. doi: 10.1002/humu.23054. 27449316
Conlan S, Park M, Deming C, Thomas PJ, Young AC, Coleman H, Sison C, NISC Comparative Sequencing Program, Weingarten RA, Lau AF, Dekker JP, Palmore TN, Frank KM, Segre JA. Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization. MBio. 2016 Jun 28;7(3). pii: e00742-16. 27353756
Soto C, Ofek G, Joyce MG, Zhang B, McKee K, Longo NS, Yang Y, Huang J, Parks R, Eudailey J, Lloyd KE, Alam SM, Haynes BF; NISC Comparative Sequencing Program, Mullikin JC, Connors M, Mascola JR, Shapiro L, Kwong PD. Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8. PLoS One. 2016 Jun 14;11(6):e0157409. 27299673
Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF. Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability. Orphanet J Rare Dis. 2016 May 14;11(1):62. doi: 10.1186/s13023-016-0439-6. 27179618
Justice CM, Bishop K, Carrington B, Mullikin JC, Swindle K, Marosy B, Sood R, Miller NH, Wilson AF. Evaluation of IRX Genes and Conserved Non-coding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis. G3 (Bethesda). 2016 Apr 13. pii: g3.116.029975. doi: 10.1534/g3.116.029975. 27172222
Oh J, Byrd AL, Park M, NISC Comparative Sequencing Program, Kong HH, Segre JA. Temporal Stability of the Human Skin Microbiome. Cell. 2016 May 5;165(4):854-66. doi: 10.1016/j.cell.2016.04.008. 27153496
Vilboux T, Malicdan MC, Chang YM, Guo J, Zerfas PM, Stephen J, Cullinane AR, Bryant J, Fischer R, Brooks BP, Zein WM, Wiggs EA, Zalewski CK, Poretti A, Bryan MM, Vemulapalli M, Mullikin JC, Kirby M, Anderson SM, NISC Comparative Sequencing Program, Huizing M, Toro C, Gahl WA, Gunay-Aygun M. Cystic cerebellar dysplasia and biallelic LAMA1 mutations: a lamininopathy associated with tics, obsessive compulsive traits and myopia due to cell adhesion and migration defects. J Med Genet. 2016 Jan 13. pii: jmedgenet-2015-103416. doi: 10.1136/jmedgenet-2015-103416. 27095636
Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S, Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R, Soto C; NISC Comparative Sequencing Program, Mullikin JC, Douek DC, Montefiori DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ, Kepler TB, Shapiro L, Ward AB4, Mascola JR, Liao HX, Kwong PD, Haynes BF. Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody. Cell. 2016 Apr 7;165(2):449-63. doi: 10.1016/j.cell.2016.02.022. Epub 2016 Mar 3. 26949186
Dotson GA; NISC Comparative Sequencing Program, Dekker JP, Palmore TN, Segre JA, Conlan S. Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence Type 111 Pseudomonas aeruginosa Strain. Genome Announc. 2016 Feb 11;4(1). pii: e01663-15. doi: 10.1128/genomeA.01663-15. 26868386
Tsai YC, Conlan S, Deming C; NISC Comparative Sequencing Program, Segre JA, Kong HH, Korlach J, Oh J. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing. MBio. 2016 Feb 9;7(1). pii: e01948-15. doi: 10.1128/mBio.01948-15. 26861018
de Filippo C, Key FM, Ghirotto S, Benazzo A, Meneu JR, Weihmann A; NISC Comparative Sequence Program, Parra G, Green ED, Andrés AM. Recent Selection Changes in Human Genes under Long-Term Balancing Selection. Mol Biol Evol. 2016 Feb 1. pii: msw023. [Epub ahead of print] 26831942
Kane MS, Davids M, Adams C, Wolfe LA, Cheung HW, Gropman A, Huang Y; NISC Comparative Sequencing Program, Ng BG, Freeze HH, Adams DR, Gahl WA, Boerkoel CF. Mitotic Intragenic Recombination: A Mechanism of Survival for Several Congenital Disorders of Glycosylation. Am J Hum Genet. 2016 Feb 4;98(2):339-46. doi: 10.1016/j.ajhg.2015.12.007. Epub 2016 Jan 21. 26805780
Boyden SE, Desai A, Cruse G, Young ML, Bolan HC, Scott LM, Eisch AR, Long RD, Lee CC, Satorius CL, Pakstis AJ, Olivera A, Mullikin JC, Chouery E, Mégarbané A, Medlej-Hashim M, Kidd KK, Kastner DL, Metcalfe DD, Komarow HD. Vibratory Urticaria Associated with a Missense Variant in ADGRE2. Engl J Med. 2016 Feb 18;374(7):656-63. doi: 10.1056/NEJMoa1500611. Epub 2016 Feb 3. 26841242
Beck TF, Mullikin JC, NISC Comparative Sequencing Program, Biesecker LG. Systematic Evaluation of Sanger Validation of NextGen Sequencing Variants. Clin Chem. 2016 Feb 4. pii: clinchem.2015.249623. [Epub ahead of print] 26847218
Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS, Jarosinski MC, Joyce MG, Lemmin TM, Leung S, Louder MK, McDaniel JR, Narpala S, Pancera M, Stuckey J, Wu X, Yang Y, Zhang B, Zhou T, NISC Comparative Sequencing Program, Mullikin JC, Baxa U, Georgiou G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L, Lee KK, Shapiro L, Mascola JR, Kwong PD. Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nat Struct Mol Biol. 2016 Jan;23(1):81-90. doi: 10.1038/nsmb.3144. Epub 2015 Dec 21. 26689967
Baran-Gale J, Kurtz CL, Erdos MR, Sison C, Young A, Fannin EE, Chines PS, Sethupathy P. Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods. Front Genet. 2015 Dec 22;6:352. doi: 10.3389/fgene.2015.00352. eCollection 2015. 26734062
Zhou Q, Wang H, Schwartz DM, Stoffels M, Park YH, Zhang Y, Yang D, Demirkaya E, Takeuchi M, Tsai WL, Layons JJ, Yu X, Ouyang C, Chen C, Chin DT, Zaal K, Chandrasekharappa SC, P Hanson E, Yu Z, Mullikin JC, Hasni SA, Wertz IE, Ombrello AK, Stone DL, Hoffmann P, Jones A, Barham BK, Leavis HL, van Royen-Kerkof A, Sibley C, Batu ED, Gül A, Siegel RM, Boehm M, Milner JD, Ozen S, Gadina M, Chae J, Laxer RM, Kastner DL, Aksentijevich I. Loss-of-function mutations in TNFAIP3 leading to A20 haploinsufficiency cause an early-onset autoinflammatory disease. Nat Genet. 2015 Dec 7. doi: 10.1038/ng.3459 26642243
Cherukuri PF, Maduro V, Fuentes-Fajardo KV, Lam K; NISC Comparative Sequencing Program, Adams DR, Tifft CJ, Mullikin JC, Gahl WA, Boerkoel CF. Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data. BMC Genomics. 2015 Nov 25;16(1):998. 26602380
Lee M, Beggs SM, Gildea D, Bupp S, Lichtenberg J, Trivedi NS; NISC Comparative Sequencing Program, Hu Y, Bodine DM, Crawford NP. Necdin is a breast cancer metastasis suppressor that regulates the transcription of c-Myc. Oncotarget. 2015 Oct 13;6(31):31557-68. 26384308
Kruszka P, Uwineza A, Mutesa L, Martinez AF, Abe Y, Zackai EH, Ganetzky R, Chung B, Stevenson RE, Adelstein RS, Ma X, Mullikin JC, Hong SK, Muenke M. Limb body wall complex, amniotic band sequence, or new syndrome caused by mutation in IQ Motif containing K (IQCK)? Mol Genet Genomic Med. 2015 Sep;3(5):424-32. 26436108
Malicdan MC, Vilboux T, Stephen J, Maglic D, Mian L, Konzman D, Guo J, Yildirimli D, Bryant J, Fischer R, Zein WM, Snow J, Vemulapalli M, Mullikin JC, Toro C7 Solomon BD, Niederhuber JE; NISC Comparative Sequencing Program, Gahl WA, Gunay-Aygun M. Mutations in human homologue of chicken talpid3 gene (KIAA0586) cause a hybrid ciliopathy with overlapping features of Jeune and Joubert syndromes. J Med Genet. 2015 Sep 18. pii: jmedgenet-2015-103316. 2638604
Hartley SW, Coon SL, Savastano LE, Mullikin JC, NISC Comparative Sequencing Program, Fu C2, Klein DC2. Neurotranscriptomics: The Effects of Neonatal Stimulus Deprivation on the Rat Pineal Transcriptome. PLoS One. 2015 Sep 14;10(9):e0137548. 26367423
Huang HW, NISC Comparative Sequencing Program, Mullikin JC, Hansen NF. Evaluation of variant detection software for pooled next-generation sequence data. BMC Bioinformatics. 2015 Jul 29;16:235. 26220471
Sood R, Hansen NF, Donovan FX, Carrington B, Bucci D, Maskeri B, Young A, Trivedi NS, Kohlschmidt J, Stone RM, Caligiuri MA, Chandrasekharappa SC, Marcucci G, Mullikin JC, Bloomfield CD5, Liu P. Somatic mutational landscape of AML with inv(16) or t(8;21) identifies patterns of clonal evolution in relapse leukemia. Leukemia. 2015 Jun 15. doi: 10.1038/leu.2015.141. 26139325
Johnston JJ, Lewis KL, Ng D, Singh LN, Wynter J, Brewer C, Brooks BP, Brownell I, Candotti F, Gonsalves SG, Hart SP, Kong HH, Rother KI, Sokolic R, Solomon BD, Zein WM, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG. Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. Am J Hum Genet. 2015 Jun 4;96(6):913-25. 26046366
Francica JR, Sheng Z, Zhang Z, Nishimura Y, Shingai M, Ramesh A, Keele BF, Schmidt SD, Flynn BJ, Darko S, Lynch RM, Yamamoto T, Matus-Nicodemos R, Wolinsky D; NISC Comparative Sequencing Program, Nason M, Valiante NM, Malyala P, De Gregorio E, Barnett SW, Singh M, O'Hagan DT, Koup RA, Mascola JR, Martin MA, Kepler TB, Douek DC, Shapiro L, Seder RA. Analysis of immunoglobulin transcripts and hypermutation following SHIV(AD8) infection and protein-plus-adjuvant immunization. Nat Commun. 2015 Apr 10;6:6565. 25858157
Zhou Q1, Yang D, Ombrello AK, Zavialov AV, Toro C, Zavialov AV, Stone DL, Chae JJ, Rosenzweig SD, Bishop K, Barron KS, Kuehn HS, Hoffmann P, Negro A, Tsai WL, Cowen EW, Pei W, Milner JD, Silvin C, Heller T, Chin DT, Patronas NJ, Barber JS, Lee CC, Wood GM, Ling A, Kelly SJ, Kleiner DE, Mullikin JC, Ganson NJ, Kong HH, Hambleton S, Candotti F, Quezado MM, Calvo KR, Alao H, Barham BK, Jones A, Meschia JF, Worrall BB, Kasner SE, Rich SS, Goldbach-Mansky R, Abinun M, Chalom E, Gotte AC, Punaro M, Pascual V, Verbsky JW, Torgerson TR, Singer NG, Gershon TR, Ozen S, Karadag O, Fleisher TA, Remmers EF, Burgess SM, Moir SL, Gadina M, Sood R, Hershfield MS, Boehm M, Kastner DL, Aksentijevich I. Early-onset stroke and vasculopathy associated with mutations in ADA2. N Engl J Med. 2014 Mar 6;370(10):911-20. 24552284
Zhou T, Lynch RM, Chen L, Acharya P, Wu X, Doria-Rose NA, Joyce MG, Lingwood D, Soto C, Bailer RT, Ernandes MJ, Kong R, Longo NS, Louder MK, McKee K, O'Dell S, Schmidt SD, Tran L, Yang Z, Druz A, Luongo TS, Moquin S, Srivatsan S, Yang Y, Zhang B, Zheng A, Pancera M, Kirys T, Georgiev IS, Gindin T, Peng HP, Yang AS; NISC Comparative Sequencing Program, Mullikin JC, Gray MD, Stamatatos L, Burton DR, Koff WC, Cohen MS, Haynes BF, Casazza JP, Connors M, Corti D, Lanzavecchia A, Sattentau QJ, Weiss RA, West AP Jr, Bjorkman PJ, Scheid JF, Nussenzweig MC, Shapiro L, Mascola JR, Kwong PD. Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell. 2015 May 20. pii: S0092-8674(15)00554-1. 26004070
Saldana-Caboverde A, Perera EM, Watkins-Chow D, Hansen NF, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Pavan WJ, Kos L. The transcription factors Ets1 and Sox10 interact during murine melanocyte development. Dev Biol. 2015 Apr 23. pii: S0012-1606(15)00212-2. 25912689
Wu X, Zhang Z, Schramm CA, Joyce MG, Do Kwon Y, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K, Georgiev IS, Chuang GY, Longo NS, Lynch RM, Saunders KO, Soto C, Srivatsan S, Yang Y, Bailer RT, Louder MK; NISC Comparative Sequencing Program, Mullikin JC, Connors M, Kwong PD, Mascola JR, Shapiro L. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell. 2015 Apr 23;161(3):470-85. 25865483
Callicrate T, Dikow R, Thomas JW, Mullikin JC, Jarvis ED, Fleischer RC1; NISC Comparative Sequencing Program. Genomic resources for the endangered Hawaiian honeycreepers. BMC Genomics. 2014 Dec 12;15:1098. 25496081
Rudd ML, Mohamed H, Price JC, O'Hara AJ, Le Gallo M, Urick ME, NISC Comparative Sequencing Program, Cruz P, Zhang S, Hansen NF, Godwin AK, Sgroi DC, Wolfsberg TG, Mullikin JC, Merino MJ, Bell DW1. Mutational analysis of the tyrosine kinome in serous and clear cell endometrial cancer uncovers rare somatic mutations in TNK2 and DDR1. BMC Cancer. 2014 Nov 26;14:884. 25427824
Oh J, Byrd AL, Deming C, Conlan S; NISC Comparative Sequencing Program, Kong HH, Segre JA. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014 Oct 2;514(7520):59-64. 25279917
Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai YC, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, NISC Comparative Sequencing Program, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med. 2014 Sep 17;6(254):254ra126. 25232178
Pemov A, Sung H, Hyland PL, Sloan JL, Ruppert SL, Baldwin AM, Boland JF, Bass SE, Lee HJ, Jones KM, Zhang X, NISC Comparative Sequencing Program, Mullikin JC, Widemann BC, Wilson AF, Stewart DR. Genetic modifiers of neurofibromatosis type 1-associated café-au-lait macule count identified using multi-platform analysis. PLoS Genet. 2014 Oct 16;10(10):e1004575. 25329635
Rudicell RS, Kwon YD, Ko SY, Pegu A, Louder MK, Georgiev IS, Wu X, Zhu J, Boyington JC, Chen X, Shi W, Yang ZY, Doria-Rose NA, McKee K, O'Dell S, Schmidt SD, Chuang GY, Druz A, Soto C, Yang Y, Zhang B, Zhou T, Todd JP, Lloyd KE, Eudailey J, Roberts KE, Donald BR, Bailer RT, Ledgerwood J, NISC Comparative Sequencing Program, Mullikin JC, Shapiro L, Koup RA, Graham BS, Nason MC, Connors M, Haynes BF, Rao SS, Roederer M, Kwong PD, Mascola JR, Nabel GJ. Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo. J Virol. 2014 Nov 1;88(21):12669-82. 25142607
Sen SK, Boelte KC, Barb JJ, Joehanes R, Zhao X, Cheng Q, Adams L, Teer JK, Accame DS, Chowdhury S, Singh LN; NISC Comparative Sequencing Program; CHARGE Consortium, Kavousi M, Peyser PA, Quigley L, Priel DL, Lau K, Kuhns DB, Yoshimura T, Johnson AD, Hwang SJ, Chen MY, Arai AE, Green ED, Mullikin JC, Kolodgie FD, O'Donnell CJ, Virmani R, Munson PJ, McVicar DW, Biesecker LG. Integrative DNA, RNA, and protein evidence connects TREML4 to coronary artery calcification. Am J Hum Genet. 2014 Jul 3;95(1):66-76. 24975946
Pierson TM, Yuan H, Marsh ED, Fuentes-Fajardo K, Adams DR, Markello T, Golas G, Simeonov DR, Holloman C, Tankovic A, Karamchandani MM, Schreiber JM, Mullikin JC; PhD for the NISC Comparative Sequencing Program, Tifft CJ, Toro C, Boerkoel CF, Traynelis SF, Gahl WA. GRIN2A mutation and early-onset epileptic encephalopathy: personalized therapy with memantine. Ann Clin Transl Neurol. 2014 Mar 1;1(3):190-198. 24839611
Lee M, Dworkin AM, Gildea D, Trivedi NS; NISC Comparative Sequencing Program, Moorhead GB, Crawford NP. RRP1B is a metastasis modifier that regulates the expression of alternative mRNA isoforms through interactions with SRSF1. Oncogene. 2014 Apr 3;33(14):1818-27. 23604122
Sen SK, Barb JJ, Cherukuri PF, Accame DS, Elkahloun AG, Singh LN, Lee-Lin SQ; NISC Comparative Sequencing Program, Kolodgie FD, Cheng Q, Zhao X, Chen MY, Arai AE, Green ED, Mullikin JC, Munson PJ, Biesecker LG. Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines. BMC Genomics. 2014 Mar 14;15:198. 24628908
Doria-Rose NA, Schramm CA, Gorman J, Moore PL, Bhiman JN, Dekosky BJ, Ernandes MJ, Georgiev IS, Kim HJ, Pancera M, Staupe RP, Altae-Tran HR, Bailer RT, Crooks ET, Cupo A, Druz A, Garrett NJ, Hoi KH, Kong R, Louder MK, Longo NS, McKee K, Nonyane M, O'Dell S, Roark RS, Rudicell RS, Schmidt SD, Sheward DJ, Soto C, Wibmer CK, Yang Y, Zhang Z, NISC Comparative Sequencing Program, Mullikin JC, Binley JM, Sanders RW, Wilson IA, Moore JP, Ward AB, Georgiou G, Williamson C, Abdool Karim SS, Morris L, Kwong PD, Shapiro L, Mascola JR. Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature. 2014 Mar 2. 24590074
Prickett TD, Zerlanko B, Gartner JJ, Parker SC, Dutton-Regester K, Lin JC, Teer JK, Wei X, Jiang J; NISC Comparative Sequencing Program, Chen G, Davies MA, Gershenwald JE, Robinson W, Robinson S, Hayward NK, Rosenberg SA, Margulies EH, Samuels Y. Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin. J Invest Dermatol. 2014 Feb;134(2):452-60. 24008424
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P; NISC Comparative Sequencing Program, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013 Dec 13;342(6164):1242592. 24337300
Oh J, Freeman AF; NISC Comparative Sequencing Program, Park M, Sokolic R, Candotti F, Holland SM, Segre JA, Kong HH. The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome Res. 2013 Dec;23(12):2103-14. 24170601
Gonsalves SG, Ng D, Johnston JJ, Teer JK, Stenson PD, Cooper DN, Mullikin JC, Biesecker LG; NISC Comparative Sequencing Program. Using exome data to identify malignant hyperthermia susceptibility mutations. Anesthesiology. 2013 Nov;119(5):1043-53. 24195946
Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N; NISC Comparative Sequencing Program, Black BL, Visel A, Pennacchio LA, Collins FS. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17921-6. 24127591
Zhu J, Wu X, Zhang B, McKee K, O'Dell S, Soto C, Zhou T, Casazza JP; NISC Comparative Sequencing Program, Mullikin JC, Kwong PD, Mascola JR, Shapiro L. De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):E4088-97. 24106303
Landouré G, Zhu PP, Lourenço CM, Johnson JO, Toro C, Bricceno KV, Rinaldi C, Meilleur KG, Sangaré M, Diallo O, Pierson TM, Ishiura H, Tsuji S, Hein N, Fink JK, Stoll M, Nicholson G, Gonzalez MA, Speziani F, Dürr A, Stevanin G, Biesecker LG, NIH Intramural Sequencing Center, Accardi J, Landis DM, Gahl WA, Traynor BJ, Marques W Jr, Züchner S, Blackstone C, Fischbeck KH, Burnett BG. Hereditary spastic paraplegia type 43 (SPG43) is caused by mutation in C19orf12. Hum Mutat. 2013 Oct;34(10):1357-60. 23857908
Johnston JJ, Wen KK, Keppler-Noreuil K, McKane M, Maiers JL, Greiner A, Sapp JC, NIH Intramural Sequencing Center, Demali KA, Rubenstein PA, Biesecker LG. Functional analysis of a de novo ACTB mutation in a patient with atypical Baraitser-Winter syndrome. Hum Mutat. 2013 Sep;34(9):1242-9. 23649928
Zhou T, Zhu J, Wu X, Moquin S, Zhang B, Acharya P, Georgiev IS, Altae-Tran HR, Chuang GY, Joyce MG, Do Kwon Y, Longo NS, Louder MK, Luongo T, McKee K, Schramm CA, Skinner J, Yang Y, Yang Z, Zhang Z, Zheng A, Bonsignori M, Haynes BF, Scheid JF, Nussenzweig MC, Simek M, Burton DR, Koff WC; NISC Comparative Sequencing Program, Mullikin JC, Connors M, Shapiro L, Nabel GJ, Mascola JR, Kwong PD. Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. Immunity. 2013 Aug 22;39(2):245-58. 23911655
Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK; NISC Comparative Sequencing Program, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13481-6. 23901115
Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG, NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program. Interpreting secondary cardiac disease variants in an exome cohort. Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. 23861362
Snitkin ES, Zelazny AM, Gupta J; NISC Comparative Sequencing Program, Palmore TN, Murray PR, Segre JA. Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment. Genome Res. 2013 Jul;23(7):1155-62. 23564252
Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, NIH Intramural Sequencing Center Comparative Sequencing Program, Kong HH, Segre JA. Topographic diversity of fungal and bacterial communities in human skin. Nature. 2013 Jun 20;498(7454):367-70. 23698366
Chandrasekharappa SC, Lach FP, Kimble DC, Kamat A, Teer JK, Donovan FX, Flynn E, Sen SK, Thongthip S, Sanborn E, Smogorzewska A, Auerbach AD, Ostrander EA; NISC Comparative Sequencing Program. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia. Blood. 2013 May 30;121(22):e138-48. 23613520
Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013 Apr 25;496(7446):469-76. 23552890
Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, Parks R, Eudailey J, Lloyd KE, Blinn J, Alam SM, Haynes BF, Simek M, Burton DR, Koff WC; NISC Comparative Sequencing Program, Mullikin JC, Mascola JR, Shapiro L, Kwong PD. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6470-5. 23536288
Teer JK, Johnston JJ, Anzick SL, Pineda M, Stone G; NISC Comparative Sequencing Program, Meltzer PS, Mullikin JC, Biesecker LG. Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting. BMC Genomics. 2013 Apr 15;14:253. 23586822
Ferreira Z, Seixas S, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Swanson WJ; NISC Comparative Sequencing Program, Clark AG, Green ED, Hurle B. Reproduction and immunity-driven natural selection in the human WFDC locus. Mol Biol Evol. 2013 Apr;30(4):938-50. 23292442
Prasad AB, Mullikin JC; NISC Comparative Sequencing Program, Green ED. A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence. Mol Phylogenet Evol. 2013 Mar;66(3):1067-74. 23247042
Solomon BD, Pineda-Alvarez DE, Hadley DW, Hansen NF, Kamat A, Donovan FX, Chandrasekharappa SC, Hong SK, Roessler E, Mullikin JC; NISC Comparative Sequencing Program. Exome Sequencing and High-Density Microarray Testing in Monozygotic Twin Pairs Discordant for Features of VACTERL Association. Mol Syndromol. 2013 Feb;4(1-2):27-31. 23653574
Ferreira Z, Hurle B, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson WJ; NISC Comparative Sequencing Program, Green ED, Clark AG, Seixas S. Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biol Evol. 2013;5(12):2512-23. 24356879
Giannuzzi G, Siswara P, Malig M, Marques-Bonet T; NISC Comparative Sequencing Program, Mullikin JC, Ventura M, Eichler EE. Evolutionary dynamism of the primate LRRC37 gene family. Genome Res. 2013 Jan;23(1):46-59. 23064749
Vester A, Velez-Ruiz G, McLaughlin HM; NISC Comparative Sequencing Program, Lupski JR, Talbot K, Vance JM, Züchner S, Roda RH, Fischbeck KH, Biesecker LG, Nicholson G, Beg AA, Antonellis A. A loss-of-function variant in the human histidyl-tRNA synthetase (HARS) gene is neurotoxic in vivo. Hum Mutat. 2013 Jan;34(1):191-9. 22930593

 

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