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In Print: Clinical Sequencing Papers of Note of the Last Two Weeks: Jan 2, 2014


The tumour suppressor gene WWOX is mutated in autosomal recessive cerebellar ataxia with epilepsy and mental retardation.
Mallaret M, Synofzik M, Lee J, Sagum CA, et al.
Brain. 2013 Dec 24. [Epub ahead of print]

Pharmacological and genomic profiling identifies NF-κB-targeted treatment strategies for mantle cell lymphoma.
Rahal R, Frick M, Romero R, Korn JM, et al.
Nat Med. 2013 Dec 22. [Epub ahead of print]

Autozygome sequencing expands the horizon of human knockout research and provides novel insights into human phenotypic variation.
Alsalem AB, Halees AS, Anazi S, Alshamekh S, Alkuraya FS.
PLoS Genet. 2013 Dec;9(12):e1004030.

Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia.
Kalender Atak Z, Gianfelici V, Hulselmans G, De Keersmaecker K, Devasia AG
PLoS Genet. 2013 Dec;9(12):e1003997.

Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy.
Van Allen EM, Foye A, Wagle N, Kim W, et al.
Prostate Cancer Prostatic Dis. 2013 Dec 24. [Epub ahead of print]

The genomic landscape of Waldenstrom's macroglobulinemia is characterized by highly recurring MYD88 and WHIM-like CXCR4 mutations, and small somatic deletions associated with B-cell lymphomagenesis.
Hunter Z, Xu L, Yang G, Zhou Y, et al.
Blood. 2013 Dec 23. [Epub ahead of print]

Whole exome sequencing in del(5q) myelodysplastic syndromes in transformation to acute myeloid leukemia.
Pellagatti A, Fernandez-Mercado M, Di Genua C, Larrayoz MJ, et al.
Leukemia. 2013 Dec 24. [Epub ahead of print]

Rapid identification of compound mutations in patients with Philadelphia-positive leukaemias by long-range next generation sequencing.
Kastner R, Zopf A, Preuner S, Pröll J, et al.
Eur J Cancer. 2013 Dec 20. [Epub ahead of print]

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma.
Okosun J, Bödör C, Wang J, Araf S, et al.
Nat Genet. 2013 Dec 22. [Epub ahead of print]

Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas.
Piotrowski A, Xie J, Liu YF, Poplawski AB, et al.
Nat Genet. 2013 Dec 22. [Epub ahead of print]

Exome sequence reveals mutations in CoA synthase as a cause of neurodegeneration with brain iron accumulation.
Dusi S, Valletta L, Haack TB, Tsuchiya Y, et al.
Am J Hum Genet. 2013 Dec 18. [Epub ahead of print]

Genome analyses of single human oocytes.
Hou Y, Fan W, Yan L, Li R, et al.
Cell. 2013 Dec 19;155(7):1492-506.

A novel null homozygous mutation confirms CACNA2D2 as a gene mutated in epileptic encephalopathy.
Pippucci T, Parmeggiani A, Palombo F, Maresca A, et al.
PLoS One. 2013 Dec 16;8(12):e82154.

Non-invasive prenatal testing of trisomies 21 and 18 by massively parallel sequencing of maternal plasma DNA in twin pregnancies.
Huang X, Zheng J, Chen M, Zhao Y, et al.
Prenat Diagn. 2013 Dec 19. [Epub ahead of print]

Fetal fraction estimate in twin pregnancies using directed cell-free DNA analysis.
Struble CA, Syngelaki A, Oliphant A, Song K, Nicolaides KH.
Fetal Diagn Ther. 2013 Dec 7. [Epub ahead of print]

Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets.
Balko JM, Giltnane J, Wang K, Schwarz LJ, et al.
Cancer Discov. 2013 Dec 19. [Epub ahead of print]

PNPLA6 mutations cause Boucher-Neuhauser and Gordon Holmes syndromes as part of a broad neurodegenerative spectrum.
Synofzik M, Gonzalez MA, Lourenco CM, Coutelier M, et al.
Brain. 2013 Dec 19. [Epub ahead of print]

HLA-DRB1, -DRB3, -DRB4 and -DRB5 genotyping at a super-high resolution level by long range PCR and high-throughput sequencing.
Ozaki Y, Suzuki S, Shigenari A, Okudaira Y, et al.
Tissue Antigens. 2014 Jan;83(1):10-6.

Pellagra-like condition is xeroderma pigmentosum/Cockayne syndrome complex and niacin confers clinical benefit.
Hijazi H, Salih MA, Hamad MH, Hassan HH, et al.
Clin Genet. 2013 Nov 21. [Epub ahead of print]

Presence of viral DNA in whole-genome sequencing of brain tumor tissues from the cancer genome atlas.
Amirian ES, Bondy ML, Mo Q, Bainbridge MN, Scheurer ME.
J Virol. 2014 Jan;88(1):774.

Exome sequencing identifies a novel EP300 frame shift mutation in a patient with features that overlap Cornelia de Lange syndrome.
Woods SA, Robinson HB, Kohler LJ, Agamanolis D, et al.
Am J Med Genet A. 2014 Jan;164(1):251-8.

De novo SCN8A mutation identified by whole-exome sequencing in a boy with neonatal epileptic encephalopathy, multiple congenital anomalies, and movement disorders.
Vaher U, Nõukas M, Nikopensius T, Kals M, et al.
J Child Neurol. 2013 Dec 18. [Epub ahead of print]

Characterization and deep sequencing analysis of exosomal and non-exosomal miRNA in human urine.
Cheng L, Sun X, Scicluna BJ, Coleman BM, Hill AF.
Kidney Int. 2013 Dec 18. [Epub ahead of print]

Whole-exome sequencing to identify a novel LMNA gene mutation associated with inherited cardiac conduction disease.
Lai CC, Yeh YH, Hsieh WP, Kuo CT, et al.
PLoS One. 2013 Dec 12;8(12):e83322.

Whole exome sequencing identifies novel recurrently mutated genes in patients with splenic marginal zone lymphoma.
Parry M, Rose-Zerilli MJ, Gibson J, Ennis S, et al.
PLoS One. 2013 Dec 13;8(12):e83244.

Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing.
Clark TG, Mallard K, Coll F, Preston M, et al.
PLoS One. 2013 Dec 11;8(12):e83012.

BRAF fusions define a distinct molecular subset of melanomas with potential sensitivity to MEK inhibition.
Hutchinson KE, Lipson D, Stephens PJ, Otto G, et al.
Clin Cancer Res. 2013 Dec 15;19(24):6696-702.

Scan statistic-based analysis of exome sequencing data identifies FAN1 at 15q13.3 as a susceptibility gene for schizophrenia and autism.
Ionita-Laza I, Xu B, Makarov V, Buxbaum JD, et al.
Proc Natl Acad Sci U S A. 2013 Dec 16. [Epub ahead of print]

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.
Malhotra A, Lindberg M, Faust GG, Leibowitz ML, et al.
Genome Res. 2013 May;23(5):762-76.

Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders.
Ladetto M, Brüggemann M, Monitillo L, Ferrero S, et al.
Leukemia. 2013 Dec 17. [Epub ahead of print]

Next generation sequencing-based expression profiling identifies signatures from benign stromal proliferations that define stromal components of breast cancer.
Guo X, Zhu SX, Brunner AL, van de Rijn M, West RB.
Breast Cancer Res. 2013 Dec 17;15(6):R117.

Non-invasive prenatal testing for fetal chromosomal abnormalities by low coverage whole genome sequencing of maternal plasma DNA: Review of 1,982 consecutive cases in a single center.
Lau TK, Cheung SW, Lo PS, Pursley AN, et al.
Ultrasound Obstet Gynecol. 2013 Dec 13. [Epub ahead of print]

Comparative microRNA profiling of prostate carcinomas with increasing tumor stage by deep-sequencing.
Hart M, Nolte E, Wach S, Szczyrba J, et al.
Mol Cancer Res. 2013 Dec 13. [Epub ahead of print]

Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus on an intensive care unit.
Price JR, Golubchik T, Cole K, Wilson DJ, et al.
Clin Infect Dis. 2013 Dec 12. [Epub ahead of print]

Next-generation sequencing for identifying pyrazinamide resistance in Mycobacterium tuberculosis.
Daum LT, Fourie PB, Bhattacharyya S, Ismail NA, et al.
Clin Infect Dis. 2013 Dec 26. [Epub ahead of print]

Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.
Johnson BE, Mazor T, Hong C, Barnes M, et al.
Science. 2013 Dec 12. [Epub ahead of print]

Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours.
Wong SQ, Li J, Salemi R, Sheppard KE, et al.
Sci Rep. 2013 Dec 13;3:3494.

Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease.
Cruchaga C, Karch CM, Jin SC, Benitez BA, et al.
Nature. 2013 Dec 11. [Epub ahead of print]

Assessment of fretal sex chromosome aneuploidy using directed cell-free DNA analysis.
Nicolaides KH, Musci TJ, Struble CA, Syngelaki A, Gil MM.
Fetal Diagn Ther. 2013 Dec 11. [Epub ahead of print]

Routine use of the Ion Torrent AmpliSeq cancer hotspot panel for identification of clinically actionable somatic mutations.
Tsongalis GJ, Peterson JD, de Abreu FB, Tunkey CD, et al.
Clin Chem Lab Med. 2013 Dec 13:1-8.

Exome sequencing reveals a novel MRE11 mutation in a patient with progressive myoclonic ataxia.
Miyamoto R, Morino H, Yoshizawa A, Miyazaki Y, et al.
J Neurol Sci. 2013 Dec 1. [Epub ahead of print]