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Recent Clinical Sequencing Papers of Note: Aug 20, 2014


Reporting tumor molecular heterogeneity in histopathological diagnosis.
Mafficini A, Amato E, Fassan M, Simbolo M, et al.
PLOS One. 2014 Aug 15;9(8):e104979.

Characterization of long non-coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing.
Malouf GG, Zhang J, Yuan Y, Compérat E, et al.
Mol Oncol. 2014 Jul 25. pii: S1574-7891(14)00162-8.

Theranostic profiling for actionable aberrations in advanced high risk osteosarcoma with aggressive biology reveals high molecular diversity: the human fingerprint hypothesis.
Egas-Bejar D, Anderson PM, Agarwal R, Corrales-Medina F, et al.
Oncoscience. 2014 Mar 12;1(2):167-179.

Genetic heterogeneity in Cornelia de Lange syndrome (CdLS) and CdLS-like phenotypes with observed and predicted levels of mosaicism.
Ansari M, Poke G, Ferry Q, Williamson K, et al.
J Med Genet. 2014 Aug 14. [Epub ahead of print]

Further evidence of the importance of RIT1 in Noonan syndrome.
Bertola DR, Yamamoto GL, Almeida TF, Buscarilli M, et al.
Am J Med Genet A. 2014 Aug 13. [Epub ahead of print]

Phenotypic overlap between familial exudative vitreoretinopathy and microcephaly, lymphedema, and chorioretinal dysplasia caused by KIF11 mutations.
Robitaille JM, Gillett RM, LeBlanc MA, Gaston D, et al.
JAMA Ophthalmol. 2014 Aug 14. [Epub ahead of print]

A novel variant in GABRB2 associated with intellectual disability and epilepsy.
Srivastava S, Cohen J, Pevsner J, Aradhya S, et al.
Am J Med Genet A. 2014 Aug 13. [Epub ahead of print]

HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations.
Usuyama N, Shiraishi Y, Sato Y, Kume H, et al.
Bioinformatics. 2014 Aug 14. [Epub ahead of print]

gCUP: Rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing.
Olejnik M, Steuwer M, Gorlatch S, Heider D.
Bioinformatics. 2014 Aug 13. [Epub ahead of print]

Deep-sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.
Jiang Y, Redmond D, Nie K, Eng KW, et al.
Genome Biol. 2014 Aug 15;15(8):432.

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C.
Dryden NH, Broome LR, Dudbridge F, Johnson N, et al.
Genome Res. 2014 Aug 13. [Epub ahead of print]

Therapeutic priority of the PI3K/AKT/mTOR pathway in small cell lung cancers as revealed by a comprehensive genomic analysis.
Umemura S, Mimaki S, Makinoshima H, Tada S, et al.
J Thorac Oncol. 2014 Sep;9(9):1324-1331.

Early-onset autosomal recessive cerebellar ataxia associated with retinal dystrophy: new human hotfoot phenotype caused by homozygous GRID2 deletion.
Van Schil K, Meire F, Karlstetter M, Bauwens M, et al.
Genet Med. 2014 Aug 14. [Epub ahead of print]

Whole exome sequencing implicates an INO80D mutation in a syndrome of aortic hypoplasia, premature atherosclerosis, and arterial stiffness.
Shameer K, Klee EW, Dalenberg AK, Kullo IJ.
Circ Cardiovasc Genet. 2014 Aug 13. [Epub ahead of print]

Unclassified renal cell carcinoma: a clinicopathological, comparative genomic hybridization, and whole-genome exon sequencing study.
Hu ZY, Pang LJ, Qi Y, Kang XL, et al.
Int J Clin Exp Pathol. 2014 Jun 15;7(7):3865-75.

RNA-seq identifies determinants of oxaliplatin sensitivity in colorectal cancer cell lines.
Li XX, Peng JJ, Liang L, Huang LY, et al.
Int J Clin Exp Pathol. 2014 Jun 15;7(7):3763-70.

PMCA4 (ATP2B4) mutation in familial spastic paraplegia.
Li M, Ho PW, Pang SY, Tse ZH, et al.
PLOS One. 2014 Aug 13;9(8):e104790.

Novel secondary somatic mutations in Ewing's sarcoma and desmoplastic small round cell tumors.
Jiang Y, Subbiah V, Janku F, Ludwig JA, et al.
PLOS One. 2014 Aug 13;9(8):e93676.

Common and rare variants in the exons and regulatory regions of osteoporosis-related genes improve osteoporotic fracture risk prediction.
Lee SH, Kang MI, Ahn SH, Lim KH, et al.
J Clin Endocrinol Metab. 2014 Aug 13 [Epub ahead of print]

Rapid identification of a novel complex I MT-ND3 m.10134C>A mutation in a Leigh syndrome patient.
Miller DK, Menezes MJ, Simons C, Riley LG, et al.
PLOS One. 2014 Aug 12;9(8):e104879.

A high-density genetic map for soybean based on specific length amplified fragment sequencing.
Qi Z, Huang L, Zhu R, Xin D, et al.
PLOS One. 2014 Aug 12;9(8):e104879.

Tectonic gene mutations in patients with Joubert syndrome.
Huppke P, Wegener E, Böhrer-Rabel H, Bolz HJ, et al.
Eur J Hum Genet. 2014 Aug 13. [Epub ahead of print]

NKX2.5 mutation identification on exome sequencing in a patient with heterotaxy.
Izumi K, Noon S, Wilkens A, Krantz ID.
Eur J Med Genet. 2014 Aug 9. [Epub ahead of print]

Identification of 33 candidate oncogenes by screening for base-specific mutations.
Tuupanen S, Hänninen UA, Kondelin J, von Nandelstadh P, et al.
Br J Cancer. 2014 Aug 12. [Epub ahead of print]

Cancer genetic testing panels for inherited cancer susceptibility: the clinical experience of a large adult genetics practice.
Selkirk CG, Vogel KJ, Newlin AC, Weissman SM, et al.
Fam Cancer. 2014 Aug 13. [Epub ahead of print]

Using RNA-seq and targeted nucleases to identify mechanisms of drug resistance in acute myeloid leukemia.
Rathe SK, Moriarity BS, Stoltenberg CB, Kurata M, et al.
Sci Rep. 2014 Aug 13;4:6048.

Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma.
Campbell CD, Mohajeri K, Malig M, Hormozdiari F, et al.
PLOS One. 2014 Aug 12;9(8):e104396.

Targeted high-throughput sequencing identifies pathogenic mutations in KCNQ4 in two large Chinese families with autosomal dominant hearing loss.
Wang H, Zhao Y, Yi Y, Gao Y, et al.
PLOS One. 2014 Aug 12;9(8):e103133.

Targeted ultra-deep sequencing reveals recurrent and mutually exclusive mutations of cancer genes in blastic plasmacytoid dendritic cell neoplasm.
Stenzinger A, Endris V, Pfarr N, Andrulis M, et al.
Oncotarget. 2014 Jul 16. [Epub ahead of print]

Mutational landscape of candidate genes in familial prostate cancer.
Johnson AM, Zuhlke KA, Plotts C, McDonnell SK, et al.
Prostate. 2014 Aug 11. [Epub ahead of print]

A novel COL4A5 mutation identified in a Chinese Han family using exome sequencing.
Xiu X, Yuan J, Deng X, Xiao J, et al.
Biomed Res Int. 2014;2014:186048.

Identification and surgical repair in a Chinese thoracic aortic aneurysm and dissection family caused by TGFBR1 mutation.
Dong SB, Zheng J, Ma WG, Chen MJ, et al.
Ann Vasc Surg. 2014 Aug 7. [Epub ahead of print]

Identify mutation in amyotrophic lateral sclerosis cases using HaloPlex target enrichment system.
Liu ZJ, Li HF, Tan GH, Tao QQ, et al.
Neurobiol Aging. 2014 Jul 11. [Epub ahead of print]

The dynamic range of circulating tumor DNA in metastatic breast cancer.
Heidary M, Auer M, Ulz P, Heitzer E, et al.
Breast Cancer Res. 2014 Aug 9;16(4):421.

Molecular pathogenesis of congenital diaphragmatic hernia revealed by exome sequencing, developmental data, and bioinformatics.
Longoni M, High FA, Russell MK, Kashani A, et al.
Proc Natl Acad Sci U S A. 2014 Aug 8. [Epub ahead of print]

Genomics of uterine leiomyomas: insights from high-throughput sequencing.
Mehine M, Mäkinen N, Heinonen HR, Aaltonen LA, Vahteristo P.
Fertil Steril. 2014 Aug 5. [Epub ahead of print]

Illumina sequencing of 15 deafness genes using fragmented amplicons.
Van Nieuwerburgh F, De Keulenaer S, De Schrijver J, Vandesompele J, et al.
BMC Res Notes. 2014 Aug 9;7(1):509.

Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics.
Heydt C, Fassunke J, Künstlinger H, Ihle MA, et al.
PLOS One. 2014 Aug 8;9(8):e104566.

Frequent cases of RAS-mutated Down syndrome acute lymphoblastic leukaemia lack JAK2 mutations.
Nikolaev SI, Garieri M, Santoni F, Falconnet E, et al.
Nat Commun. 2014 Aug 8;5:4654.

Exome sequencing identifies a recurrent de novo ZSWIM6 mutation associated with acromelic frontonasal dysostosis.
Smith JD, Hing AV, Clarke CM, Johnson NM, et al.
Am J Hum Genet. 2014 Aug 7;95(2):235-240.

Mutations in LAMA1 cause cerebellar dysplasia and cysts with and without retinal dystrophy.
Aldinger KA, Mosca SJ, Tétreault M, Dempsey JC, et al.
Am J Hum Genet. 2014 Aug 7;95(2):227-234.

High-throughput sequencing of TCR repertoires in multiple sclerosis reveals intrathecal enrichment of EBV-reactive CD8+ T cells.
Lossius A, Johansen JN, Vartdal F, Robins H, et al.
Eur J Immunol. 2014 Aug 7. [Epub ahead of print]

Whole genome sequencing of glioblastoma multiforme identifies multiple structural variations involved in EGFR activation.
Furgason JM, Li W, Milholland B, Cross E, et al.
Mutagenesis. 2014 Aug 6. [Epub ahead of print]