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In Print: Last Week's Clinical Sequencing Papers of Note: Sep 26, 2012

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LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker.
Chen D, Sun Y, Wei Y, Zhang P, et al.
Nat Med. 2012 Sep 23. [Epub ahead of print]


Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis.
Busque L, Patel JP, Figueroa ME, Vasanthakumar A, et al.
Nat Genet. 2012 Sep 23. [Epub ahead of print]


Comprehensive molecular portraits of human breast tumours.
The Cancer Genome Atlas Network; Genome sequencing centres: Washington University in St Louis, Koboldt DC, Fulton RS, McLellan MD, Schmidt H, et al.
Nature. 2012 Sep 23. [Epub ahead of print]


A novel VCP mutation as the cause of atypical IBMPFD in a Chinese family.
Gu JM, Ke YH, Yue H, Liu YJ, et al.
Bone. 2012 Sep 18. pii: S8756-3282(12)01236-7.


Recurrent somatic mutations in human gastric cancers identified by whole exome sequencing.
Shimizu T, Marusawa H, Chiba T.
Gastroenterology. 2012 Sep 20. pii: S0016-5085(12)01383-2.


Nonsense mutations in AAGAB cause punctate palmoplantar keratoderma type Buschke-Fischer-Brauer.
Giehl KA, Eckstein GN, Pasternack SM, Praetzel-Wunder S, et al.
Am J Hum Genet. 2012 Sep 19. pii: S0002-9297(12)00465-X.


A hypermorphic missense mutation in PLCG2, encoding phospholipase Cγ2, causes a dominantly inherited autoinflammatory disease with immunodeficiency.
Zhou Q, Lee GS, Brady J, Datta S, et al.
Am J Hum Genet. 2012 Sep 18. pii: S0002-9297(12)00418-1.


A noncoding, regulatory mutation implicates HCFC1 in nonsyndromic intellectual disability.
Huang L, Jolly LA, Willis-Owen S, Gardner A, et al.
Am J Hum Genet. 2012 Sep 18. pii: S0002-9297(12)00423-5.


High throughput DNA sequencing to detect differences in the subgingival plaque microbiome in elderly subjects with and without dementia.
Cockburn AF, Dehlin JM, Ngan T, Crout R, et al.
Investig Genet. 2012 Sep 21;3(1):19.


Whole-transcriptome analysis reveals established and novel associations with TMPRSS2:ERG fusion in prostate cancer.
Chow A, Amemiya Y, Sugar L, Nam R, Seth A.
Anticancer Res. 2012 Sep;32(9):3629-41.


Universal amplification, next-generation sequencing and assembly of HIV-1 genomes.
Gall A, Ferns B, Morris C, Watson S, et al.
J Clin Microbiol. 2012 Sep 19. [Epub ahead of print]


Targeted sequence capture and high-throughput sequencing in the molecular diagnosis of ichthyosis and other skin diseases.
Scott CA, Plagnol V, Nitoiu D, Bland PJ, et al.
J Invest Dermatol. 2012 Sep 20. [Epub ahead of print]


Clonal evolution of high-grade serous ovarian carcinoma from primary to recurrent disease.
Castellarin M, Milne K, Zeng T, Tse K, et al.
J Pathol. 2012 Sep 21. [Epub ahead of print]
2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Trisomy 13 detection in the first trimester of pregnancy using a chromosome-selective cell-free DNA analysis method.
Ashoor G, Syngelaki A, Wang E, Struble C, et al.
Ultrasound Obstet Gynecol. 2012 Sep 20. [Epub ahead of print]


Ultra-deep sequencing reveals hidden HIV-1 minority lineages and shifts of viral population between the main cellular reservoirs of the infection after therapy interruption.
Rozera G, Abbate I, Ciccozzi M, Lo Presti A, et al.
J Med Virol. 2012 Jun;84(6):839-44.


An informatics approach to analyzing the incidentalome.
Berg JS, Adams M, Nassar N, Bizon C, et al.
Genet Med. 2012 Sep 20. [Epub ahead of print]


Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer.
Murphy SJ, Cheville JC, Zarei S, Johnson SH, et al.
DNA Res. 2012 Sep 18. [Epub ahead of print]


Rab25 is a tumor suppressor gene with anti-angiogenic and anti-invasive activities in esophageal squamous cell carcinoma.
Tong M, Chan KW, Bao JY, Wong KY, et al.
Cancer Res. 2012 Sep 18. [Epub ahead of print]


Deep sequencing does not reveal additional transmitted mutations in patients diagnosed with HIV-1 variants with single nucleoside reverse transcriptase inhibitor resistance mutations..
Pingen M, van der Ende M, Wensing A, El Barzouhi A, et al.
HIV Med. 2012 Sep 19. [Epub ahead of print]


WDR35 mutation in siblings with Sensenbrenner syndrome: A ciliopathy with variable phenotype.
Bacino CA, Dhar SU, Brunetti-Pierri N, Lee B, Bonnen PE.
Am J Med Genet A. 2012 Sep 17. [Epub ahead of print]


Missense mutations in ITPR1 cause autosomal dominant congenital nonprogressive spinocerebellar ataxia.
Huang L, Warman J, Carter MT, Friend KL, et al.
Orphanet J Rare Dis. 2012 Sep 17;7(1):67.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.