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In Print: Last Week's Clinical Sequencing Papers of Note: Dec 19, 2012


Should genetic findings from genome research be reported back to the participants?
Steinsbekk KS, Solberg B.
Tidsskr Nor Laegeforen. 2012 Oct 16;132(19):2190-3.

Effective assessment of EGFR mutation status in bronchoalveolar lavage and pleural fluids by next generation sequencing.
Buttitta F, Felicioni L, Del Grammastro M, Filice G, et al.
Clin Cancer Res. 2012 Dec 14. [Epub ahead of print]

Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer.
Ruark E, Snape K, Humburg P, Loveday C, et al.
Nature. 2012 Dec 16. [Epub ahead of print]

Whole-exome sequencing of a unique brain malformation with periventricular heterotopia, cingulate polymicrogyria and midbrain tectal hyperplasia.
Okumura A, Hayashi M, Shimojima K, Ikeno M, et al.
Neuropathology. 2012 Dec 13. [Epub ahead of print]

Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer.
Kreso A, O'Brien CA, van Galen P, Gan O, et al.
Science. 2012 Dec 13. [Epub ahead of print]

Whole-genome reconstruction and mutational signatures in gastric cancer.
Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, et al.
Genome Biol. 2012 Dec 13;13(12):R115.

RNA-seq of human breast ductal carcinoma in situ models reveals aldehyde dehydrogenase isoform 5A1 as a novel potential target.
Kaur H, Mao S, Li Q, Sameni M, et al.
PLoS One. 2012;7(12):e50249.

Recessive mutations in SPTBN2 implicate β-III spectrin in both cognitive and motor development.
Lise S, Clarkson Y, Perkins E, Kwasniewska A, et al.
PLoS Genet. 2012 Dec;8(12):e1003074.

Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach.
Ding D, Lou X, Hua D, Yu W, et al.
PLoS Genet. 2012 Dec;8(12):e1003065.

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.
Zankari E, Hasman H, Kaas RS, Seyfarth AM, et al.
J Antimicrob Chemother. 2012 Dec 11. [Epub ahead of print]

Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data.
Parker M, Chen X, Bahrami A, Dalton J, et al.
Genome Biol. 2012 Dec 11;13(12):R113.

Hemizygous mutations in SNAP29 unmask autosomal recessive conditions and contribute to atypical findings in patients with 22q11.2DS.
McDonald-McGinn DM, Fahiminiya S, Revil T, Nowakowska BA, et al.
J Med Genet. 2012 Dec 11. [Epub ahead of print]

Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing.
Liu Q, Shen E, Min Q, Li X, et al.
BMC Genomics. 2012 Dec 11;13(1):692.

Expression of small nucleolar RNAs in leukemic cells.
Teittinen KJ, Laiho A, Uusimäki A, Pursiheimo JP, et al.
Cell Oncol (Dordr) . 2012 Nov 15. [Epub ahead of print]

Spectrum of non-tuberculous mycobacteria identified using standard biochemical testing vs. 16S sequencing.
Chihota VN, van Halsema CL, Grant AD, Fielding KL, et al.
Int J Tuberc Lung Dis. 2012 Dec 8. [Epub ahead of print]

Derivation of HLA types from shotgun sequence datasets.
Warren RL, Choe G, Freeman DJ, Castellarin M, et al.
Genome Med. 2012 Dec 10;4(12):95.

Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome.
Jiang B, Liang X, Chen Y, Ma T, et al.
Sci Rep. 2012;2:936.

microRNA expression profile of peripheral blood mononuclear cells of Klinefelter syndrome.
Sui W, Ou M, Chen J, Li H, et al.
Exp Ther Med. 2012 Nov;4(5):825-831.

Whole-exome sequencing efficiently detects rare mutations in autosomal recessive nonsyndromic hearing loss.
Diaz-Horta O, Duman D, Foster J 2nd, Sırmacı A, et al.
PLoS One. 2012;7(11):e50628.

Deep clonal profiling of formalin fixed paraffin embedded clinical samples.
Holley T, Lenkiewicz E, Evers L, Tembe W, et al.
PLoS One. 2012;7(11):e50586.

Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA.
Plebani R, Oliver GR, Trerotola M, Guerra E, et al.
Neoplasia. 2012 Nov;14(11):1087-96.

The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma.
Stead LF, Berri S, Wood HM, Egan P, et al.
Neoplasia. 2012 Nov;14(11):1075-86.

Progressive cerebellar atrophy and polyneuropathy: expanding the spectrum of PNKP mutations.
Poulton C, Oegema R, Heijsman D, Hoogeboom J, et al.
Neurogenetics. 2012 Dec 9. [Epub ahead of print]

Rapid hepatitis C virus divergence among chronically infected individuals.
Cruz-Rivera M, Carpio-Pedroza JC, Escobar-Gutiérrez A, Lozano D, et al.
J Clin Microbiol. 2012 Dec 5. [Epub ahead of print]

Efficient depletion of host DNA contamination in malaria clinical sequencing.
Oyola SO, Gu Y, Manske M, Otto TD, et al.
J Clin Microbiol. 2012 Dec 5. [Epub ahead of print]

High frequency of GATA2 mutations in patients with mild chronic neutropenia evolving to MonoMac syndrome, myelodysplasia and acute myeloid leukemia.
Pasquet M, Bellanné-Chantelot C, Tavitian S, Prade N, et al.
Blood. 2012 Dec 6. [Epub ahead of print]

Emergence and global spread of epidemic healthcare-associated Clostridium difficile.
He M, Miyajima F, Roberts P, Ellison L, et al.
Nat Genet. 2012 Dec 9. [Epub ahead of print]

Mutations in GNAL cause primary torsion dystonia.
Fuchs T, Saunders-Pullman R, Masuho I, Luciano MS, et al.
Nat Genet. 2012 Dec 9. [Epub ahead of print]

Recurrent SETBP1 mutations in atypical chronic myeloid leukemia.
Piazza R, Valletta S, Winkelmann N, Redaelli S, et al.
Nat Genet. 2012 Dec 9. [Epub ahead of print]

Rare allelic forms of PRDM9 associated with childhood leukemogenesis.
Hussin J, Sinnett D, Casals F, Idaghdour Y, et al.
Genome Res. 2012 Dec 5. [Epub ahead of print]

Genetic alterations in advanced HBV-related HCC with portal vein tumor thrombosis: Insights from next generation DNA sequencing.
Chaiteerakij R, Roberts LR.
J Hepatol. 2012 Dec 6. [Epub ahead of print]

Whole exome sequencing in foetal akinesia expands the genotype-phenotype spectrum of GBE1 glycogen storage disease mutations.
Ravenscroft G, Thompson EM, Todd EJ, Yau KS, et al.
Neuromuscul Disord. 2012 Dec 3. [Epub ahead of print]

Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities.
Talkowski ME, Maussion G, Crapper L, Rosenfeld JA, et al.
Am J Hum Genet. 2012 Dec 7;91(6):1128-34.

Cowchock syndrome is associated with a mutation in apoptosis-inducing factor.
Rinaldi C, Grunseich C, Sevrioukova IF, Schindler A, et al.
Am J Hum Genet. 2012 Dec 7;91(6):1095-102.

Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.
Xue Y, Chen Y, Ayub Q, Huang N, et al.
Am J Hum Genet. 2012 Dec 7;91(6):1022-1032.

A catalogue of glioblastoma and brain microRNAs identified by deep sequencing.
Hua D, Mo F, Ding D, Li L, et al.
OMICS. 2012 Dec;16(12):690-9.

Clinical diagnosis by whole-genome sequencing of a prenatal sample.
Talkowski ME, Ordulu Z, Pillalamarri V, Benson CB, Blumenthal I, Connolly S, Hanscom C, Hussain N, Pereira S, Picker J, Rosenfeld JA, et al.
N Engl J Med. 2012 Dec 6;367(23):2226-32.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.