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In Print: Last Week's Clinical Sequencing Papers of Note: Jul 10, 2013


BRAF/NRAS wild-type melanomas have a high mutation load correlating with histological and molecular signatures of UV damage.
Mar VJ, Wong SQ, Li J, Scolyer RA, et al.
Clin Cancer Res. 2013 Jul 5. [Epub ahead of print]

Germline missense variants in the BTNL2 gene are associated with prostate cancer susceptibility.
Fitzgerald LM, Kumar A, Boyle EA, Zhang Y, et al.
Cancer Epidemiol Biomarkers Prev. 2013 Jul 5. [Epub ahead of print]

Somatic SETBP1 mutations in myeloid malignancies.
Makishima H, Yoshida K, Nguyen N, Przychodzen B, et al.
Nat Genet. 2013 Jul 7. [Epub ahead of print]

Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia.
Sakaguchi H, Okuno Y, Muramatsu H, Yoshida K, et al.
Nat Genet. 2013 Jul 7. [Epub ahead of print]

Targeted resequencing analysis of 25 genes commonly mutated in myeloid disorders in del(5q) myelodysplastic syndromes.
Fernandez-Mercado M, Burns A, Pellagatti A, Giagounidis A, et al.
Haematologica. 2013 Jul 5. [Epub ahead of print]

Predicting the functional consequences of non-synonymous DNA sequence variants − evaluation of bioinformatics tools and development of a consensus strategy.
Frousios K, Iliopoulos CS, Schlitt T, Simpson MA.
Genomics. 2013 Jul 3. [Epub ahead of print]

Mutations in AQP5, encoding a water-channel protein, cause autosomal-dominant diffuse nonepidermolytic palmoplantar keratoderma.
Blaydon DC, Lind LK, Plagnol V, Linton KJ, et al.
Am J Hum Genet. 2013 Jul 2. [Epub ahead of print]

Recessive TRAPPC11 Mutations Cause a Disease Spectrum of Limb Girdle Muscular Dystrophy and Myopathy with Movement Disorder and Intellectual Disability.
Bögershausen N, Shahrzad N, Chong JX, von Kleist-Retzow JC, et al.
Am J Hum Genet. 2013 Jul 2. [Epub ahead of print]

Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing.
Hollegaard MV, Grauholm J, Nielsen R, Grove J, et al.
Mol Genet Metab. 2013 Jun 13. [Epub ahead of print]

Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.
Chen R, Giliani S, Lanzi G, Mias GI, et al.
Allergy Clin Immunol. 2013 Jul 4. [Epub ahead of print]

Oral bacterial community dynamics in paediatric patients with malignancies in relation to chemotherapy-related oral mucositis: a prospective study.
Ye Y, Carlsson G, Agholme MB, Wilson JA, et al.
Clin Microbiol Infect. 2013 May 31. [Epub ahead of print]

Identification of Three Novel ECEL1 Mutations in Three Families with Distal Arthrogryposis Type 5D.
Shaheen R, Al-Owain M, Khan AO, Aglan M, et al.
Clin Genet. 2013 Jul 6. [Epub ahead of print]

SCN2A Mutation Is Associated With Infantile Spasms and Bitemporal Glucose Hypometabolism.
Sundaram SK, Chugani HT, Tiwari VN, Huq AH.
Pediatr Neurol. 2013 Jul;49(1):46-9.

Whole exome sequencing revealed biallelic IFT122 mutations in a family with CED1 and recurrent pregnancy loss.
Tsurusaki Y, Yonezawa R, Furuya M, Nishimura G, et al.
Clin Genet. 2013 Jul 5. [Epub ahead of print]

Prioritizing Potentially Druggable Mutations with dGene: An Annotation Tool for Cancer Genome Sequencing Data.
Kumar RD, Chang LW, Ellis MJ, Bose R.
PLoS One. 2013 Jun 27;8(6):e67980.

An Integrated Diagnosis Strategy for Congenital Myopathies.
Böhm J, Vasli N, Malfatti E, Le Gras S, et al.
PLoS One. 2013 Jun 24;8(6):e67527.

Serum Antibody Repertoire Profiling Using In Silico Antigen Screen.
Liu X, Hu Q, Liu S, Tallo LJ, et al.
PLoS One. 2013 Jun 27;8(6):e67181.

Characterizing the Genetic Basis for Nicotine Induced Cancer Development: A Transcriptome Sequencing Study.
Bavarva JH, Tae H, Settlage RE, Garner HR.
PLoS One. 2013 Jun 18;8(6):e67252.

A mutation in TGFB3 associated with a syndrome of low muscle mass, growth retardation, distal arthrogryposis and clinical features overlapping with Marfan and Loeys-Dietz syndrome.
Rienhoff HY Jr, Yeo CY, Morissette R, Khrebtukova I, et al.
Am J Med Genet A. 2013 Jul 3. [Epub ahead of print]

Deep Sequencing the MicroRNA Transcriptome in Colorectal Cancer.
Schee K, Lorenz S, Worren MM, Günther CC, et al.
PLoS One. 2013 Jun 18;8(6):e66165.

The Mycobacterium tuberculosis regulatory network and hypoxia.
Galagan JE, Minch K, Peterson M, Lyubetskaya A, et al.
Nature. 2013 Jul 3. [Epub ahead of print]

Whole-genome sequencing in health care. Recommendations of the European Society of Human Genetics.
van El CG, Cornel MC, Borry P, Hastings RJ, et al.
Eur J Hum Genet. 2013 Jun;21 Suppl 1:S1-5.

Single Cell Analysis of Lymph Node Tissue from HIV-1 Infected Patients Reveals that the Majority of CD4+ T-cells Contain One HIV-1 DNA Molecule.
Josefsson L, Palmer S, Faria NR, Lemey P, et al.
PLoS Pathog. 2013 Jun;9(6):e1003432.

Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer.
Ovaska K, Matarese F, Grote K, Charapitsa I, et al.
PLoS Comput Biol. 2013 Jun;9(6):e1003100.

Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing.
Zhang J, Liu J, Sun J, Chen C, et al.
Brief Bioinform. 2013 Jul 1. [Epub ahead of print]

Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals.
Cassa CA, Tong MY, Jordan DM.
Hum Mutat. 2013 Jul 1. [Epub ahead of print]

The syndrome of Microcornea, Myopic Chorioretinal Atrophy and Telecanthus (MMCAT) Is Caused by Mutations in ADAMTS18.
Aldahmesh MA, Alshammari MJ, Khan AO, Mohamed JY, et al.
Hum Mutat. 2013 Jul 1. [Epub ahead of print]

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma.
Jones DT, Hutter B, Jäger N, Korshunov A, et al.
Nat Genet. 2013 Jun 30. [Epub ahead of print]

Intraclonal heterogeneity is a critical early event in the development of myeloma and precedes the development of clinical symptoms.
Walker BA, Wardell CP, Melchor L, Brioli A, et al.
Leukemia. 2013 Jul 2. [Epub ahead of print]

Compound heterozygosity of predicted loss-of-function DES variants in a family with recessive desminopathy.
McLaughlin HM, Kelly MA, Hawley PP, Darras BT, et al.
BMC Med Genet. 2013 Jul 2;14(1):68.

Coffin-Siris syndrome is a SWI/SNF complex disorder.
Tsurusaki Y, Okamoto N, Ohashi H, Mizuno S, et al.
Clin Genet. 2013 Jul 1. [Epub ahead of print]

Protective Role of IL6 in Vascular Remodeling in Schistosoma-Pulmonary Hypertension.
Graham BB, Chabon J, Kumar R, Kolosionek E, et al.
Am J Respir Cell Mol Biol. 2013 Jul 1. [Epub ahead of print]

Mutations in LYRM4, encoding iron-sulfur cluster biogenesis factor ISD11, cause deficiency of multiple respiratory chain complexes.
Lim SC, Friemel M, Marum JE, Tucker EJ, et al.
Hum Mol Genet. 2013 Jun 28. [Epub ahead of print]

Severe infantile Leigh syndrome associated with a rare mitochondrial ND6 mutation, m.14487T>C.
Tarnopolsky M, Meaney B, Robinson B, Sheldon K, Boles RG.
Am J Med Genet A. 2013 Jun 27. [Epub ahead of print]

West syndrome, microcephaly, grey matter heterotopia and hypoplasia of corpus callosum due to a novel ARFGEF2 mutation.
Banne E, Atawneh O, Henneke M, Brockmann K, et al.
J Med Genet. 2013 Jun 28. [Epub ahead of print]

FGFR1 mutations cause Hartsfield syndrome, the unique association of holoprosencephaly and ectrodactyly.
Simonis N, Migeotte I, Lambert N, Perazzolo C, et al.
J Med Genet. 2013 Jun 28. [Epub ahead of print]

Targeted next generation sequencing in SPAST-negative hereditary spastic paraplegia.
Kumar KR, Blair NF, Vandebona H, Liang C, et al.
J Neurol. 2013 Jun 28. [Epub ahead of print]

Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens.
Spencer DH, Sehn JK, Abel HJ, Watson MA, et al.
J Mol Diagn. 2013 Jun 25. [Epub ahead of print]

Clinical Validation of a Next-Generation Sequencing Screen for Mutational Hotspots in 46 Cancer-Related Genes.
Singh RR, Patel KP, Routbort MJ, Reddy N, et al.
J Mol Diagn. 2013 Jun 25. [Epub ahead of print]

Mutations in PIK3R1 Cause SHORT Syndrome.
Dyment DA, Smith AC, Alcantara D, Schwartzentruber JA, et al.
Am J Hum Genet. 2013 Jun 24. [Epub ahead of print]

SHORT Syndrome with Partial Lipodystrophy Due to Impaired Phosphatidylinositol 3 Kinase Signaling.
Chudasama KK, Winnay J, Johansson S, Claudi T, et al.
Am J Hum Genet. 2013 Jun 24. [Epub ahead of print]

PIK3R1 Mutations Cause Syndromic Insulin Resistance with Lipoatrophy.
Thauvin-Robinet C, Auclair M, Duplomb L, Caron-Debarle M, et al.
Am J Hum Genet. 2013 Jun 24. [Epub ahead of print]

Deep intronic 'mutations' cause hemophilia A: Application of Next Generation Sequencing in patients without detectable mutation in F8 cDNA.
Pezeshkpoor B, Zimmer N, Marquardt N, Nanda I, et al.
J Thromb Haemost. 2013 Jun 29. [Epub ahead of print]

Nautilus: a Bioinformatics Package for the Analysis of HIV-1 Targeted Deep Sequencing Data.
Kijak GH, Pham P, Sanders-Buell EE, Harbolick EA, et al.
AIDS Res Hum Retroviruses. 2013 Jun 28. [Epub ahead of print]