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In Print: Last Week's Clinical Sequencing Papers of Note: Dec 5, 2012


Next generation sequencing of CLU, PICALM and CR1: pitfalls and potential solutions.
Lord J, Turton J, Medway C, Shi H, et al.
Int J Mol Epidemiol Genet. 2012;3(4):262-75.

Whole-exome sequencing identifies mutated PCK2 and HUWE1 associated with carcinoma cell proliferation in a hepatocellular carcinoma patient.
Liu YX, Zhang SF, Ji YH, Guo SJ, et al.
Oncol Lett. 2012 Oct;4(4):847-851.

A single-nucleotide substitution mutator phenotype revealed by exome sequencing of human colon adenomas.
Nikolaev SI, Sotiriou SK, Pateras IS, Santoni F, et al.
Cancer Res. 2012 Dec 1;72(23):6279-6289.

Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma.
Sausen M, Leary RJ, Jones S, Wu J, et al.
Nat Genet. 2012 Dec 2. [Epub ahead of print]

Massively parallel sequencing of enriched target amplicons for high-resolution genotyping of Salmonella serovars.
Singh P, Foley SL, Nayak R, Kwon YM.
Mol Cell Probes. 2012 Nov 29. [Epub ahead of print]

Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual disability syndrome.
Basel-Vanagaite L, Dallapiccola B, Ramirez-Solis R, Segref A, et al.
Am J Hum Genet. 2012 Nov 28. [Epub ahead of print]

Mutations in Ano3 cause dominant craniocervical dystonia: ion channel implicated in pathogenesis.
Charlesworth G, Plagnol V, Holmström KM, Bras J, et al.
Am J Hum Genet. 2012 Nov 27. [Epub ahead of print]

Noninvasive fetal trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies.
Jiang F, Ren J, Chen F, Zhou Y, et al.
BMC Med Genomics. 2012 Dec 1;5(1):57.

Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing.
Leary RJ, Sausen M, Kinde I, Papadopoulos N, et al.
Sci Transl Med. 2012 Nov 28;4(162):162ra154.

Genome-wide screen for aberrantly expressed miRNAs reveals miRNA profile signature in breast cancer.
Guo L, Zhao Y, Yang S, Cai M, et al.
Mol Biol Rep. 2012 Nov 30. [Epub ahead of print]

Exome sequencing in a family with restless legs syndrome.
Weissbach A, Siegesmund K, Brüggemann N, Schmidt A, et al.
Mov Disord. 2012 Nov;27(13):1686-9.

Fetal aneuploidy screening by maternal plasma DNA sequencing: 'False positive' due to confined placental mosaicism.
Choi H, Lau TK, Jiang FM, Chan MK, et al.
Prenat Diagn. 2012 Nov 27. [Epub ahead of print]

Exome analysis identified a novel mutation in the RBP4 gene in a consanguineous pedigree with retinal dystrophy and developmental abnormalities.
Cukras C, Gaasterland T, Lee P, Gudiseva HV, et al.
PLoS One. 2012;7(11):e50205.

A homozygous mutation of C12orf65 causes spastic paraplegia with optic atrophy and neuropathy (SPG55).
Shimazaki H, Takiyama Y, Ishiura H, Sakai C, et al.
J Med Genet. 2012 Dec;49(12):777-84.

High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing.
Halbritter J, Diaz K, Chaki M, Porath JD, et al.
J Med Genet. 2012 Dec;49(12):756-67.

Whole-transcriptome sequencing identifies novel IRF2BP2-CDX1 fusion gene brought about by translocation t(1;5)(q42;q32) in mesenchymal chondrosarcoma.
Nyquist KB, Panagopoulos I, Thorsen J, Haugom L, et al.
PLoS One. 2012;7(11):e49705.

Genome-wide profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays.
Srinivasan S, Patil AH, Verma M, Bingham JL, Srivatsan R.
J Clin Bioinforma. 2012 Nov 26;2(1):21.

High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.
Xiao YL, Kash JC, Beres SB, Sheng ZM, et al.
J Pathol. 2012 Nov 26. [Epub ahead of print]

Combinational usage of next generation sequencing and qPCR for the analysis of tumour samples.
Loewe RP.
Methods. 2012 Nov 20. [Epub ahead of print]

Mutation in TECPR2 reveals a role for autophagy in hereditary spastic paraparesis.
Oz-Levi D, Ben-Zeev B, Ruzzo EK, Hitomi Y, et al.
Am J Hum Genet. 2012 Nov 20. [Epub ahead of print]

Alteration of fatty-acid-metabolizing enzymes affects mitochondrial form and function in hereditary spastic paraplegia.
Tesson C, Nawara M, Salih MA, Rossignol R, et al.
Am J Hum Genet. 2012 Nov 20. [Epub ahead of print]

Exome sequencing reveals de novo WDR45 mutations causing a phenotypically distinct, X-linked dominant form of NBIA.
Haack TB, Hogarth P, Kruer MC, Gregory A, et al.
Am J Hum Genet. 2012 Nov 20. [Epub ahead of print]

Germline mutation in EXPH5 implicates the Rab27B effector protein Slac2-b in inherited skin fragility.
McGrath JA, Stone KL, Begum R, Simpson MA, et al.
Am J Hum Genet. 2012 Nov 20. [Epub ahead of print]

Weighted pedigree-based statistics for testing the association of rare variants.
Shugart YY, Zhu Y, Guo W, Xiong M.
BMC Genomics. 2012 Nov 24;13(1):667.

The Scan

Should've Been Spotted Sooner

Scientists tell the Guardian that SARS-CoV-2 testing issues at a UK lab should have been noticed earlier.

For Martian Fuel

Researchers have outlined a plan to produce rocket fuel on Mars that uses a combination of sunlight, carbon dioxide, frozen water, cyanobacteria, and engineered E. coli, according to Gizmodo.

To Boost Rapid Testing

The Washington Post writes that new US programs aim to boost the availability of rapid at-home SARS-CoV-2 tests.

PNAS Papers on Strawberry Evolution, Cell Cycle Regulators, False-Positive Triplex Gene Editing

In PNAS this week: strawberry pan-genome, cell cycle-related roles for MDM2 and MDMX, and more.