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In Print: Clinical Sequencing Papers of Note of the Last Two Weeks: Nov 28, 2012

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Rapid whole-genome sequencing for the investigation of a suspected tuberculosis outbreak.
Török ME, Reuter S, Bryant J, Köser CU, et al.
J Clin Microbiol. 2012 Nov 21.


Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing.
Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK.
BMC Genomics. 2012 Nov 21;13(1):649.


Longitudinal analysis of the lung Microbiome in lung transplantation.
Borewicz K, Pragman AA, Kim HB, Hertz M, et al.
FEMS Microbiol Lett. 2012 Nov 22. doi: 10.1111/1574-6968.12053.


Genome and transcriptome sequencing in prospective refractory metastatic triple negative breast cancer uncovers therapeutic vulnerabilities.
Craig DW, O'Shaughnessy JA, Kiefer JA, Aldrich J, et al.
Mol Cancer Ther. 2012 Nov 19.


Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements.
Hooper SD, Jiao X, Sundström E, Rehman FL, et al.
BMC Res Notes. 2012 Nov 22;5(1):648.


Adult siblings with homozygous G6PC3 mutations expand our understanding of the severe congenital neutropenia type 4 (SCN4) phenotype.
Fernandez BA, Green JS, Bursey F, Barrett B, et al.
BMC Med Genet. 2012 Nov 21;13(1):111.


Genomic analysis of Meckel-Gruber syndrome in Arabs reveals marked genetic heterogeneity and novel candidate genes.
Shaheen R, Faqeih E, Alshammari MJ, Swaid A, et al.
Eur J Hum Genet. 2012 Nov 21. doi: 10.1038/ejhg.2012.254.


Exome sequencing identifies a branch point variant in Aarskog-Scott syndrome.
Aten E, Sun Y, Almomani R, Santen GW, et al.
Hum Mutat. 2012 Nov 21. doi: 10.1002/humu.22252.


Whole exome sequencing in a patient with uniparental disomy of chromosome 2 and a complex phenotype.
Carmichael H, Shen Y, Nguyen TT, Hirschhorn JN, Dauber A.
Clin Genet. 2012 Nov 21. doi: 10.1111/cge.12064.


Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.
Archer J, Weber J, Henry K, Winner D, et al.
PLoS One. 2012;7(11):e49602. doi: 10.1371/journal.pone.0049602. Epub 2012 Nov 14.


Discovery of a novel polyomavirus in acute diarrheal samples from children.
Yu G, Greninger AL, Isa P, Phan TG, et al.
PLoS One. 2012;7(11):e49449. doi: 10.1371/journal.pone.0049449. Epub 2012 Nov 14.


Characterization of chromatin structure-associated histone modifications in breast cancer cells.
Hong CP, Choe MK, Roh TY.
Genomics Inform. 2012 Sep;10(3):145-52. doi: 10.5808/GI.2012.10.3.145. Epub 2012 Sep 28.


A unified method for detecting secondary trait associations with rare variants: application to sequence data.
Liu DJ, Leal SM.
PLoS Genet. 2012 Nov;8(11):e1003075. doi: 10.1371/journal.pgen.1003075. Epub 2012 Nov 15.


Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome.
Wambach JA, Wegner DJ, Depass K, Heins H, Druley et al.
Pediatrics. 2012 Nov 19.


Secondary mutations in BRCA2 associated with clinical resistance to a PARP inhibitor.
Barber LJ, Sandhu S, Chen L, Campbell J, et al.
J Pathol. 2012 Nov 20. doi: 10.1002/path.4140.


Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.
Stubbs A, McClellan EA, Horsman S, Hiltemann SD, et al.
J Clin Bioinforma. 2012 Nov 19;2(1):19.


Perspectives of clinical genetics professionals toward genome sequencing and incidental findings: A survey study.
Lemke A, Bick D, Dimmock D, Simpson P, Veith R.
Clin Genet. 2012 Nov 20. doi: 10.1111/cge.12060.


Atlas2 Cloud: a framework for personal genome analysis in the cloud.
Evani US, Challis D, Yu J, Jackson AR, et al.
BMC Genomics. 2012 Oct 26;13 Suppl 6:S19. doi: 10.1186/1471-2164-13-S6-S19. Epub 2012 Oct 26.


Haploinsufficiency at the human IFNGR2 locus contributes to mycobacterial disease.
Kong XF, Vogt G, Itan Y, Macura-Biegun A, et al.
Hum Mol Genet. 2012 Nov 16.


Focal facial dermal dysplasia, type IV, is caused by mutations in CYP26C1.
Slavotinek AM, Mehrotra P, Nazarenko I, Tang PL, et al.
Hum Mol Genet. 2012 Nov 16.


Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.
O'Roak BJ, Vives L, Fu W, Egertson JD, et al.
Science. 2012 Nov 15.


Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes.
Albrechtsen A, Grarup N, Li Y, Sparsø T, et al.
Diabetologia. 2012 Nov 19.


Whole exome sequencing identified a novel zinc-finger gene ZNF141 associated with autosomal recessive postaxial polydactyly type A.
-Kalsoom UE, Klopocki E, Wasif N, Tariq M, et al.
J Med Genet. 2012 Nov 17.


B cell exchange across the blood-brain barrier in multiple sclerosis.
von Büdingen HC, Kuo TC, Sirota M, van Belle CJ, et al.
J Clin Invest. 2012 Nov 19. pii: 63842. doi: 10.1172/JCI63842.


Low abundance drug resistance variants in transmitted HIV drug resistance surveillance specimens identified using tagged pooled pyrosequencing.
Ji H, Li Y, Graham M, Liang B, et al.
J Virol Methods. 2012 Nov 14. pii: S0166-0934(12)00382-5. doi: 10.1016/j.jviromet.2012.10.018.


Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data.
Spencer DH, Abel HJ, Lockwood CM, Payton JE, et al.
J Mol Diagn. 2012 Nov 13. pii: S1525-1578(12)00259-0. doi: 10.1016/j.jmoldx.2012.08.001.


Recurrent de novo mutations in PACS1 cause defective cranial-neural-crest migration and define a recognizable intellectual-disability syndrome.
Schuurs-Hoeijmakers JH, Oh EC, Vissers LE, Swinkels ME, et al.
Am J Hum Genet. 2012 Nov 14. pii: S0002-9297(12)00536-8. doi: 10.1016/j.ajhg.2012.10.013.


Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.
Harris SR, Cartwright EJ, Török ME, Holden MT, et al.
Lancet Infect Dis. 2012 Nov 9. pii: S1473-3099(12)70268-2. doi: 10.1016/S1473-3099(12)70268-2.


Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.
Walker TM, Ip CL, Harrell RH, Evans JT, et al.
Lancet Infect Dis. 2012 Nov 14. pii: S1473-3099(12)70277-3. doi: 10.1016/S1473-3099(12)70277-3.


SRY mutation analysis by next generation (deep) sequencing in a cohort of chromosomal Disorders of Sex Development (DSD) patients with a mosaic karyotype.
Hersmus R, Stoop H, Turbitt E, Oosterhuis JW, et al.
BMC Med Genet. 2012 Nov 16;13(1):108.


Exome analysis of two limb-girdle muscular dystrophy families: mutations identified and challenges encountered.
McDonald KK, Stajich J, Blach C, Ashley-Koch AE, Hauser MA.
PLoS One. 2012;7(11):e48864. doi: 10.1371/journal.pone.0048864. Epub 2012 Nov 14.


An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia.
Gruber TA, Larson Gedman A, Zhang J, Koss CS, et al.
Cancer Cell. 2012 Nov 13;22(5):683-97. doi: 10.1016/j.ccr.2012.10.007.


A 3.7 Mb deletion encompassing ZEB2 causes a novel polled and multisystemic syndrome in the progeny of a somatic mosaic bull.
Capitan A, Allais-Bonnet A, Pinton A, Marquant-Le Guienne B, et al.
PLoS One. 2012;7(11):e49084. Epub 2012 Nov 9.


Novel mutation in VCP gene causes atypical amyotrophic lateral sclerosis.
González-Pérez P, Cirulli ET, Drory VE, Dabby R, et al.
Neurology. 2012 Nov 14.


Identification of a novel gene fusion RNF213‑SLC26A11 in chronic myeloid leukemia by RNA-seq.
Zhou JB, Zhang T, Wang BF, Gao HZ, Xu X.
Mol Med Report. 2012 Nov 13. doi: 10.3892/mmr.2012.1183.


TREM2 variants in Alzheimer's disease.
Guerreiro R, Wojtas A, Bras J, Carrasquillo M, et al.
N Engl J Med. 2012 Nov 14.


Linking genome annotation projects with genetic disorders using ontologies.
Legaz-García MD, Miñarro-Giménez JA, Madrid M, Menárguez-Tortosa M, Torres Martínez S.
J Med Syst. 2012 Nov 14.


A direct comparison of next generation sequencing enrichment methods using an aortopathy gene ganel- clinical diagnostics perspective.
Wooderchak-Donahue WL, O'Fallon BD, Furtado LV, Durtschi JD, et al.
BMC Med Genomics. 2012 Nov 14;5(1):50.


Exome sequencing in tracking clonal evolution in multiple myeloma following therapy.
Weston-Bell N, Gibson J, John M, Ennis S, Pfeifer S, et al.
Leukemia. 2012 Oct 9. doi: 10.1038/leu.2012.287.


Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.
Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, et al.
PLoS Negl Trop Dis. 2012 Oct;6(10):e1853. Epub 2012 Oct 25.


Next-generation cDNA screening for oncogene and resistance phenotypes.
Shindoh N, Yoda A, Yoda Y, Sullivan TJ, et al.
PLoS One. 2012;7(11):e49201. Epub 2012 Nov 7.


Loss-of-function mutations in IGSF1 cause an X-linked syndrome of central hypothyroidism and testicular enlargement.
Sun Y, Bak B, Schoenmakers N, van Trotsenburg AS, et al.
Nat Genet. 2012 Nov 11. doi: 10.1038/ng.2453.


The genetic landscape of mutations in Burkitt lymphoma.
Love C, Sun Z, Jima D, Li G, et al.
Nat Genet. 2012 Nov 11. doi: 10.1038/ng.2468.


Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing.
The ICGC MMML-Seq Project, Richter J, Schlesner M, Hoffmann S, Kreuz M, et al.
Nat Genet. 2012 Nov 11. doi: 10.1038/ng.2469.


Clinical and histopathological study of Charcot-Marie-Tooth neuropathy with a novel S90W mutation in BSCL2.
Choi BO, Park MH, Chung KW, Woo HM, et al.
Neurogenetics. 2012 Nov 10.


Acrocallosal syndrome: identification of a novel KIF7 mutation and evidence for oligogenic inheritance.
Walsh DM, Shalev SA, Simpson MA, Morgan NV, et al.
Eur J Med Genet. 2012 Nov 6. pii: S1769-7212(12)00282-0. doi: 10.1016/j.ejmg.2012.10.004.


Late onset of symptoms in an atypical patient with the cblJ inborn error of vitamin B(12) metabolism: Diagnosis and novel mutation revealed by exome sequencing.
Kim JC, Lee NC, Hwu PW, Chien YH, et al.
Mol Genet Metab. 2012 Oct 16. pii: S1096-7192(12)00373-3. doi: 10.1016/j.ymgme.2012.10.005.


DHTKD1 mutations cause 2-aminoadipic and 2-oxoadipic aciduria.
Danhauser K, Sauer SW, Haack TB, Wieland T, et al.
Am J Hum Genet. 2012 Nov 6. pii: S0002-9297(12)00528-9. doi: 10.1016/j.ajhg.2012.10.006.


Defective presynaptic choline transport underlies hereditary motor neuropathy.
Barwick KE, Wright J, Al-Turki S, McEntagart MM, et al.
Am J Hum Genet. 2012 Nov 6. pii: S0002-9297(12)00529-0. doi: 10.1016/j.ajhg.2012.09.019.

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