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In Print: Last Week's Clinical Sequencing Papers of Note: Apr 10, 2013


Practices and policies of clinical exome sequencing providers: analysis and implications.
Jamal SM, Yu JH, Chong JX, Dent KM, et al.
Am J Med Genet A. 2013 Apr 5. [Epub ahead of print]

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
McLean JS, Lombardo MJ, Ziegler MG, Novotny M, et al.
Genome Res. 2013 Apr 5. [Epub ahead of print]

SMIM1 underlies the Vel blood group and influences red blood cell traits.
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, et al.
Nat Genet. 2013 Apr 7. [Epub ahead of print]

Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA.
Murtaza M, Dawson SJ, Tsui DW, Gale D, et al.
Nature. 2013 Apr 7. [Epub ahead of print]

Deficiency of the E3 ubiquitin ligase TRIM2 in early-onset axonal neuropathy.
Ylikallio E, Pöyhönen R, Zimon M, De Vriendt E, et al.
Hum Mol Genet. 2013 Apr 4. [Epub ahead of print]

Mosaicism of the UDP-galactose transporter SLC35A2 causes a congenital disorder of glycosylation.
Ng BG, Buckingham KJ, Raymond K, Kircher M, et al.
Am J Hum Genet. 2013 Apr 4;92(4):632-6.

Hypomorphic mutations in PGAP2, encoding a GPI-anchor-remodeling protein, cause autosomal-recessive intellectual disability.
Hansen L, Tawamie H, Murakami Y, Mang Y, et al.
Am J Hum Genet. 2013 Apr 4;92(4):575-83.

Whole-exome sequencing links caspase recruitment domain 11 (CARD11) inactivation to severe combined immunodeficiency.
Greil J, Rausch T, Giese T, Bandapalli OR, et al.
J Allergy Clin Immunol. 2013 Apr 3. [Epub ahead of print]

Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer.
Grant RC, Al-Sukhni W, Borgida AE, Holter S, et al.
Hum Genomics. 2013 Apr 5;7(1):11.

Tumor associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing.
Heitzer E, Ulz P, Belic J, Gutschi S, et al.
Genome Med. 2013 Apr 5;5(4):30.

Detection of novel mutations that cause autosomal dominant retinitis pigmentosa in candidate genes by long-range PCR amplification and next-generation sequencing.
Dias Mde S, Hernan I, Pascual B, Borràs E, et al.
Mol Vis. 2013;19:654-64.

Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome.
Ajmal M, Khan MI, Neveling K, Tayyab A, et al.
Mol Vis. 2013;19:644-53.

ACMG statement on noninvasive prenatal screening for fetal aneuploidy.
The Noninvasive Prenatal Screening Work Group of the American College of Medical Genetics and Genomics, et al.
Genet Med. 2013 Apr 4. [Epub ahead of print]

Description and pilot results from a novel method for evaluating return of incidental findings from next-generation sequencing technologies.
Goddard KA, Whitlock EP, Berg JS, Williams MS, et al.
Genet Med. 2013 Apr 4. [Epub ahead of print]

Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics.
Danzer M, Niklas N, Stabentheiner S, Hofer K, et al.
BMC Genomics. 2013 Apr 4;14(1):221.

Genome and bioinformatic analysis of a HAdV-B14p1 virus isolated from a baby with pneumonia in Beijing, China.
Tang L, An J, Xie Z, Dehghan S, et al.
PLoS One. 2013;8(3):e60345.

Whole genome sequence analysis of the first Australian OXA-48-producing outbreak-associated Klebsiella pneumonia isolates: the resistome and in vivo evolution.
Espedido BA, Steen JA, Ziochos H, Grimmond SM, et al.
PLoS One. 2013;8(3):e59920.

Clustering and alignment of polymorphic sequences for HLA-DRB1 genotyping.
Ringquist S, Bellone G, Lu Y, Roeder K, Trucco M.
PLoS One. 2013;8(3):e59835.

Discovery analysis of TCGA data reveals association between germline genotype and survival in ovarian cancer patients.
Braun R, Finney R, Yan C, Chen QR, et al.
PLoS One. 2013;8(3):e55037.

Epigenomic alterations in localized and advanced prostate cancer.
Lin PC, Giannopoulou EG, Park K, Mosquera JM, et al.
Neoplasia. 2013 Apr;15(4):373-83.

Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness.
Mokili JL, Dutilh BE, Lim YW, Schneider BS, et al.
PLoS One. 2013;8(3):e58404.

Simple and efficient identification of rare recessive pathologically important sequence variants from next generation exome sequence data.
Carr IM, Morgan J, Watson C, Melnik S, et al.
Hum Mutat. 2013 Mar 28. [Epub ahead of print]

Re-analysis of an original CMTX3 family using exome sequencing identifies a known BSCL2 mutation.
Chaudhry R, Kidambi A, Brewer MH, Antonellis A, et al.
Muscle Nerve. 2012 Nov 29. [Epub ahead of print]

NUBPL mutations in patients with complex I deficiency and a distinct MRI pattern.
Kevelam SH, Rodenburg RJ, Wolf NI, Ferreira P, et al.
Neurology. 2013 Apr 3. [Epub ahead of print]

Secondary findings from non-invasive prenatal testing for common fetal aneuploidies by whole genome sequencing as a clinical service.
Lau TK, Jiang FM, Stevenson RJ, Lo TK, et al.
Prenat Diagn. 2013 Apr 2. [Epub ahead of print]

Proximal dominant hereditary motor and sensory neuropathy with proximal dominance association with mutation in the TRK-fused gene.
Lee SS, Lee HJ, Park JM, Hong YB, et al.
JAMA Neurol. 2013 Mar 18:1-9.

Support for the N-methyl-D-aspartate receptor hypofunction hypothesis of schizophrenia from exome sequencing in multiplex families.
Timms AE, Dorschner MO, Wechsler J, Choi KY, et al.
JAMA Psychiatry. 2013 Apr 3:1-9.

Dissecting the genotype in syndromic intellectual disability using whole exome sequencing in addition to genome-wide copy number analysis.
Classen CF, Riehmer V, Landwehr C, Kosfeld A, et al.
Hum Genet. 2013 Apr 4. [Epub ahead of print]

Exome sequencing identifies a novel INPPL1 mutation in opsismodysplasia.
Iida A, Okamoto N, Miyake N, Nishimura G, et al.
J Hum Genet. 2013 Apr 4. [Epub ahead of print]

Exome sequencing reveals a novel ANO10 mutation in a Japanese patient with autosomal recessive spinocerebellar ataxia.
Maruyama H, Morino H, Miyamoto R, Murakami N, et al.
Clin Genet. 2013 Apr 4. [Epub ahead of print]

Whole genome sequencing identifies SCN2A mutation in monozygotic twins with Ohtahara syndrome and unique neuropathologic findings.
Touma M, Joshi M, Connolly MC, Ellen Grant P, et al.
Epilepsia. 2013 Mar 28. [Epub ahead of print]

Next-generation sequencing: proof of concept for antenatal prediction of the fetal Kell blood group phenotype from cell-free fetal DNA in maternal plasma.
Rieneck K, Bak M, Jønson L, Clausen FB, et al.
Transfusion. 2013 Apr 3. [Epub ahead of print]

Impaired epidermal ceramide synthesis causes autosomal recessive congenital ichthyosis and reveals the importance of ceramide acyl chain length.
Eckl KM, Tidhar R, Thiele H, Oji V, et al.
J Invest Dermatol. 2013 Apr 2. [Epub ahead of print]

Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia.
Qian M, Jin W, Zhu X, Jia X, et al.
J Hematol Oncol. 2013 Apr 2;6(1):25.

A closer look at the recommended criteria for disclosing genetic results: perspectives of medical genetic specialists, genomic researchers, and institutional review board chairs.
Brandt DS, Shinkunas L, Hillis SL, Daack-Hirsch SE, et al.
J Genet Couns. 2013 Apr 2. [Epub ahead of print]

Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients.
Tanskanen T, Gylfe AE, Katainen R, Taipale M, et al.
Scand J Gastroenterol. 2013 Apr 2. [Epub ahead of print]