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In Print: Last Week's Clinical Sequencing Papers of Note: Dec 11, 2013


Identification of CHIP as a novel causative gene for autosomal recessive cerebellar ataxia.
Shi Y, Wang J, Li JD, Ren H, et al.
PLoS One. 2013 Dec 2;8(12):e81884.

Linkage study and exome sequencing identify a BDP1 mutation associated with hereditary hearing loss.
Girotto G, Abdulhadi K, Buniello A, Vozzi D, et al.
PLoS One. 2013 Dec 2;8(12):e80323.

Motivations for undertaking DNA sequencing-based non-invasive prenatal testing for fetal aneuploidy: a qualitative study with early adopter patients in Hong Kong.
Yi H, Hallowell N, Griffiths S, Yeung Leung T.
PLoS One. 2013 Nov 27;8(11):e81794.

Multilayered molecular profiling supported the monoclonal origin of metastatic renal cell carcinoma.
Huang Y, Gao S, Wu S, Song P, et al.
Int J Cancer. 2013 Dec 6. [Epub ahead of print]

Preferences for results delivery from exome sequencing/genome sequencing.
Wright MF, Lewis KL, Fisher TC, Hooker GW, et al.
Genet Med. 2013 Dec 5. [Epub ahead of print

The genomic landscape of oesophagogastric junctional adenocarcinoma.
Chong IY, Cunningham D, Barber LJ, Campbell J, et al.
J Pathol. 2013 Nov;231(3):301-10.

Minimal residual disease monitoring with high-throughput sequencing of T cell receptors in cutaneous T cell lymphoma.
Weng WK, Armstrong R, Arai S, Desmarais C, et al.
Sci Transl Med. 2013 Dec 4;5(214):214ra171.

Next generation sequencing in nonsyndromic intellectual disability: From a negative molecular karyotype to a possible causative mutation detection.
Athanasakis E, Licastro D, Faletra F, Fabretto A, et al.
Am J Med Genet A. 2013 Dec 4. [Epub ahead of print]

Robust diagnostic genetic testing using solution capture enrichment and a novel variant-filtering interface.
Watson CM, Crinnion LA, Morgan JE, Harrison SM, et al.
Hum Mutat. 2013 Dec 4. [Epub ahead of print]

Diagnostic exome sequencing identifies two novel IQSEC2 mutations associated with X-linked intellectual disability with seizures: implications for genetic counseling and clinical diagnosis.
Gandomi SK, Farwell Gonzalez KD, Parra M, Shahmirzadi L, et al.
J Genet Couns. 2013 Dec 4. [Epub ahead of print]

Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control.
Guo Y, Sheng Q, Samuels DC, Lehmann B, et al.
Biomed Res Int. 2013;2013:915636. Epub 2013 Nov 4.

Germline mutations of inhibins in early-onset ovarian epithelial tumors.
Tournier I, Marlin R, Walton K, Charbonnier F, et al.
Hum Mutat. 2013 Dec 2. [Epub ahead of print]

Excess congenital non-synonymous variation in leukemia-associated genes in MLL- infant leukemia: a children's oncology group report.
Valentine MC, Linabery AM, Chasnoff S, Hughes AE, et al.
Leukemia. 2013 Dec 4. [Epub ahead of print]

VHL mosaicism can be detected by clinical next-generation sequencing and is not restricted to patients with a mild phenotype.
Coppin L, Grutzmacher C, Crépin M, Destailleur E, et al.
Eur J Hum Genet. 2013 Dec 4. [Epub ahead of print]

Further delineation of the SATB2 phenotype.
Döcker D, Schubach M, Menzel M, Munz M, et al.
Eur J Hum Genet. 2013 Dec 4. [Epub ahead of print]

Exome sequencing identifies Laing distal myopathy MYH7 mutation in a Roma family previously diagnosed with distal neuronopathy.
Komlósi K, Hadzsiev K, Garbes L, Martínez Carrera LA, et al.
Neuromuscul Disord. 2013 Nov 11. [Epub ahead of print]

Diagnostic validation of a familial hypercholesterolaemia cohort provides a model for using targeted next generation DNA sequencing in the clinical setting.
Hinchcliffe M, Le H, Fimmel A, Molloy L, et al.
Pathology. 2013 Dec 1. [Epub ahead of print]

Targeted high-throughput sequencing identifies a TARDBP mutation as a cause of early-onset FTD without motor neuron disease.
Synofzik M, Born C, Rominger A, Lummel N, et al.
Neurobiol Aging. 2013 Oct 29. [Epub ahead of print]

Confirmation of cause and manner of death via a comprehensive cardiac autopsy including whole exome next-generation sequencing.
Loporcaro CG, Tester DJ, Maleszewski JJ, Kruisselbrink T, Ackerman MJ.
Arch Pathol Lab Med. 2013 Dec 3. [Epub ahead of print]

IgM repertoire biodiversity is reduced in HIV-1 infection and systemic lupus erythematosus.
Yin L, Hou W, Liu L, Cai Y, et al.
Front Immunol. 2013 Nov 15;4:373.

RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma.
Smallridge RC, Chindris AM, Asmann YW, Casler JD, et al.
J Clin Endocrinol Metab. 2013 Dec 2. [Epub ahead of print]

Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing.
Mostafavi S, Battle A, Zhu X, Potash JB, et al.
Mol Psychiatry. 2013 Dec 3. [Epub ahead of print]

Whole exome sequencing in splenic marginal zone lymphoma reveals mutations in genes involved in marginal zone differentiation.
Martínez N, Almaraz C, Vaqué JP, Varela I, et al.
Leukemia. 2013 Dec 3. [Epub ahead of print]

Computational optimisation of targeted DNA sequencing for cancer detection.
Martinez P, McGranahan N, Birkbak NJ, Gerlinger M, Swanton C.
Sci Rep. 2013 Dec 3;3:3309.

Noninvasive prenatal testing for whole fetal chromosomal aneuploidies: a multicenter prospective cohort trial in Taiwan.
Shaw SW, Hsiao CH, Chen CY, Ren Y, et al.
Fetal Diagn Ther. 2013 Nov 30. [Epub ahead of print]

Whole exome sequencing of pancreatic neoplasms with acinar differentiation.
Jiao Y, Yonescu R, Offerhaus GJ, Klimstra DS, et al.
J Pathol. 2013 Nov 29. [Epub ahead of print]

Next generation sequencing to dissect hereditary nephrotic syndrome in mice identifies a hypomorphic mutation in Lamb2 and models Pierson syndrome.
Bull KR, Mason T, Rimmer AJ, Crockford TL, et al.
J Pathol. 2013 Nov 29. [Epub ahead of print]

Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing.
Radovich M, Clare SE, Atale R, Pardo I, et al.
Breast Cancer Res Treat. 2013 Nov 29. [Epub ahead of print]

TTC7A mutations disrupt intestinal epithelial apicobasal polarity.
Bigorgne AE, Farin HF, Lemoine R, Mahlaoui N, et al.
J Clin Invest. 2013 Dec 2. pii: 71471. [Epub ahead of print]

EIF2AK4 mutations cause pulmonary veno-occlusive disease, a recessive form of pulmonary hypertension.
Eyries M, Montani D, Girerd B, Perret C, et al.
Nat Genet. 2013 Dec 1. [Epub ahead of print]

Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups.
India Project Team of the International Cancer Genome Consortium, Maitra A, Biswas NK, et al.
Nat Commun. 2013 Dec 2;4:2873.

The genetic basis of DOORS syndrome: an exome-sequencing study.
Campeau PM, Kasperaviciute D, Lu JT, Burrage LC, et al.
Lancet Neurol. 2013 Nov 28. [Epub ahead of print]

Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes.
Lohmueller KE, Sparsø T, Li Q, Andersson E, et al.
Am J Hum Genet. 2013 Nov 26. [Epub ahead of print]

SAMS, a syndrome of short stature, auditory-canal atresia, mandibular hypoplasia, and skeletal abnormalities is a unique neurocristopathy caused by mutations in goosecoid.
Parry DA, Logan CV, Stegmann AP, Abdelhamed ZA, et al.
Am J Hum Genet. 2013 Nov 23. [Epub ahead of print]