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Recent Clinical Sequencing Papers of Note: Sep 10, 2014

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Targeted gene panel sequencing in children with very early onset inflammatory bowel disease-evaluation and prospective analysis.
Kammermeier J, Drury S, James CT, Dziubak R, et al.
J Med Genet. 2014 Sep 5. [Epub ahead of print]


Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data.
Chiba K, Shiraishi Y, Nagata Y, Yoshida K, et al.
Bioinformatics. 2014 Sep 4. [Epub ahead of print]


Genome sequencing of idiopathic pulmonary fibrosis in conjunction with a medical school human anatomy course.
Kumar A, Dougherty M, Findlay GM, Geisheker M, et al.
PLOS One. 2014 Sep 5;9(9):e106744.


Synaptotagmin 2 mutations cause an autosomal-dominant form of Lambert-Eaton myasthenic syndrome and nonprogressive motor neuropathy.
Herrmann DN, Horvath R, Sowden JE, Gonzales M, et al.
Am J Hum Genet. 2014 Sep 4;95(3):332-339.


Mutations in FEZF1 cause Kallmann syndrome.
Kotan LD, Hutchins BI, Ozkan Y, Demirel F, et al.
Am J Hum Genet. 2014 Sep 4;95(3):326-331.


CCDC151 mutations cause primary ciliary dyskinesia by disruption of the outer dynein arm docking complex formation.
Hjeij R, Onoufriadis A, Watson CM, Slagle CE, et al.
Am J Hum Genet. 2014 Sep 4;95(3):257-274.


Genomic characterisation of small cell lung cancer patient-derived xenografts generated from endobronchial ultrasound-guided transbronchial needle aspiration specimens.
Leong TL, Marini KD, Rossello FJ, Jayasekara SN, et al.
PLOS One. 2014 Sep 5;9(9):e106862.


A dominant mutation in hexokinase 1 (HK1) causes retinitis pigmentosa.
Sullivan LS, Koboldt DC, Bowne SJ, Lang S, et al.
Invest Ophthalmol Vis Sci. 2014 Sep 4. [Epub ahead of print]


Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours.
Rakheja D, Chen KS, Liu Y, Shukla AA, et al.
Nat Commun. 2014 Sep 5;2:4802.


Genome-wide identification and expression analysis of microRNA involved in small cell lung cancer via deep sequencing.
Yan C, Shi X, Wang Q, Wang Y, et al.
Mol Med Rep. 2014 Sep 4. [Epub ahead of print]


Whole-genome sequencing of Asian lung cancers: second-hand smoke unlikely to be responsible for higher incidence of lung cancer among Asian never-smokers.
Krishnan VG, Ebert PJ, Ting JC, Lim E, et al.
Cancer Res. 2014 Sep 4. [Epub ahead of print]


The mutational pattern of primary lymphoma of the central nervous system determined by whole exome sequencing.
Vater I, Montesinos-Rongen M, Schlesner M, Haake A, et al.
Leukemia. 2014 Sep 5. [Epub ahead of print]


Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.
Sowalsky AG, Xia Z, Wang L, Zhao H, et al.
Mol Cancer Res. 2014 Sep 4. [Epub ahead of print]


Linkage analysis and whole-exome sequencing exclude extra mutations responsible for the parkinsonian phenotype of spinocerebellar ataxia-2.
Wang C, Xu Y, Feng X, Ma J, et al.
Neurobiol Aging. 2014 Aug 2. [Epub ahead of print]


Novel genetic mutations in a sporadic port-wine stain.
Lian CG, Sholl LM, Zakka LR, O TM, et al.
JAMA Dermatol. 2014 Sep 3. [Epub ahead of print]


A probabilistic model to predict clinical phenotypic traits from genome sequencing.
Chen YC, Douville C, Wang C, Niknafs N, et al.
PLOS Comput Biol. 2014 Sep 4;10(9):e1003825.


Molecular pathology: SC18-1 interesting case – actionable mutation I a case with a recurrent pleomorphic xanthoastrocytoma with anaplastic features.
Harada S, Fallon KB, Reddy A, Nabors LB.
Pathology. 2014 Oct;46 Suppl 2:S28-S29.


Research resources: comparative microRNA profiles in human corona radiata cells and cumulus oophorus cells detected by next-generation small RNA sequencing.
Tong XH, Xu B, Zhang YW, Liu YS, Ma CH.
PLOS One. 2014 Sep 4;9(9):e106706.


Association of exome sequences with plasma C-reactive protein levels in >9,000 participants.
Schick UM, Auer PL, Bis JC, Lin H, et al.
Hum Mol Genet. 2014 Sep 3. [Epub ahead of print]


Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
Goldstein JI, Fredrik Jarskog L, Hilliard C, Alfirevic A, et al.
Nat Commun. 2014 Sep 4;5:4757.


Novel CHKB mutation expands the megaconial muscular dystrophy phenotype.
Cabrera-Serrano M, Junckerstorff RC, Atkinson V, Sivadorai P, et al.
Muscle Nerve. 2014 Sep 3. [Epub ahead of print]


Systems consequences of amplicon formation in human breast cancer.
Inaki K, Menghi F, Woo XY, Wagner JP, et al.
Genome Res. 2014 Sep 3. [Epub ahead of print]


Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel.
Tung N, Battelli C, Allen B, Kaldate R, et al.
Cancer. 2014 Sep 3. [Epub ahead of print]


Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin-fixed, paraffin-embedded tissue.
Gailey MP, Stence AA, Jensen CS, Ma D.
Cancer Cytopathol. 2014 Sep 3. [Epub ahead of print]


Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome.
Zemojtel T, Köhler S, Mackenroth L, Jäger M, et al.
Sci Transl Med. 2014 Sep 3;6(252):252ra123.


Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer.
Rothé F, Laes JF, Lambrechts D, Smeets D, et al.
The Ann Oncol. 2014 Jul 25. [Epub ahead of print]


Expression profiling of exosomal miRNAs derived from human esophageal cancer cells by Solexa high-throughput sequencing.
Liao J, Liu R, Yin L, Pu Y.
Int J Mol Sci. 2014 Sep 2;15(9):15530-15551.


ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media.
Blakeway LV, Power PM, Jen FE, Worboys SR, et al.
FASEB J. 2014 Sep 2. [Epub ahead of print]


Network analysis of ChIP-seq data reveals key genes in prostate cancer.
Zhang Y, Huang Z, Zhu Z, Liu J, et al.
Eur J Med Res. 2014 Sep 3;19(1):47.


RNA-seq reveals aurora kinase driven-mTOR pathway activation in patients with sarcomatoid metastatic renal cell carcinoma.
Pal SK, He M, Tong T, Wu H, et al.
Mol Cancer Res. 2014 Sep 2. [Epub ahead of print]


A novel variant in TBX20 (p.D176N) identified by whole-exome sequencing in combination with a congenital heart disease related gene filter is associated with familial atrial septal defect.
Liu JJ, Fan LL, Chen JL, Tan ZP, Yang YF.
J Zhejiang Univ Sci B. 2014 Sept.;15(9):830-837.


ANO10 mutations cause ataxia and coenzyme Q10 deficiency.
Balreira A, Boczonadi V, Barca E, Pyle A, et al.
J Neurol. 2014 Sep 3. [Epub ahead of print]


Whole exome sequence analysis of Peters anomaly.
Weh E, Reis LM, Happ HC, Levin AV, et al.
Hum Genet. 2014 Sep 3. [Epub ahead of print]


Identification and characterization of novel serum microRNA candidates from deep sequencing in cervical cancer patients.
Juan L, Tong HL, Zhang P, Guo G, et al.
Sci Rep. 2014 Sep 3;4:6277.


Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer.
Arthur JC, Gharaibeh RZ, Mühlbauer M, Perez-Chanona E, et al.
Nat Commun. 2014 Sep 3;5:4724.


The expanding spectrum of PRPS1-associated phenotypes: three novel mutations segregating with X-linked hearing loss and mild peripheral neuropathy.
Robusto M, Fang M, Asselta R, Castorina P, et al.
Eur J Hum Genet. 2014 Sep 3. [Epub ahead of print]


Recessive ACTA1 variant causes congenital muscular dystrophy with rigid spine.
O'Grady GL, Best HA, Oates EC, Kaur S, et al.
Eur J Hum Genet. 2014 Sep 3. [Epub ahead of print]


Genetic diagnosis of two dopa-responsive dystonia families by exome sequencing.
Sun ZF, Zhang YH, Guo JF, Sun QY, et al.
PLOS One. 2014 Sep 2;9(9):e106388.


Application of multi-objective optimization to pooled experiments of next generation sequencing for detection of rare mutations.
Zilinskas J, Lančinskas A, Guarracino MR.
PLOS One. 2014 Sep 2;9(9):e104992.


Exome sequencing reveals a mutation in DMP1 in a family with familial sclerosing bone dysplasia.
Gannagé-Yared MH, Makrythanasis P, Chouery E, Sobacchi C, et al.
Bone. 2014 Aug 30. [Epub ahead of print]


Exome sequencing identifies SLC17A9 pathogenic gene in two Chinese pedigrees with disseminated superficial actinic porokeratosis.
Cui H, Li L, Wang W, Shen J, et al.
J Med Genet. 2014 Sep 1. [Epub ahead of print]


Transient abnormal myelopoiesis/acute megakaryoblastic leukemia diagnosed in the placenta of a stillborn Down syndrome fetus with targeted next generation sequencing.
Federmann B, Fasan A, Kagan KO, Haen S, Fend F.
Leukemia. 2014 Sep 2. [Epub ahead of print]


Targeted analysis of whole genome sequence data to diagnose genetic cardiomyopathy.
Golbus JR, Puckelwartz MJ, Dellefave-Castillo L, Fahrenbach JP, et al.
Circ Cardiovasc Genet. 2014 Sep 1. [Epub ahead of print]


What you are missing could matter: a rare, complex BRAF mutation affecting codons 599, 600, and 601 uncovered by next generation sequencing.
Wilson MA, Morrissette JJ, McGettigan S, Roth D, et al.
Cancer Genet. 2014 Jun 18. [Epub ahead of print]


Detection of aneuploidy from single fetal nucleated red blood cells using whole genome sequencing.
Hua R, Barrett AN, Tan TZ, Huang Z, et al.
Prenat Diagn. 2014 Sep 1. [Epub ahead of print]


Several fusion genes identified by whole transcriptome sequencing in a spindle cell sarcoma with rearrangements of chromosome arm 12q and MDM2 amplification.
Panagopoulos I, Bjerkehagen B, Gorunova L, Berner JM, et al.
Int J Oncol. 2014 Aug 18. [Epub ahead of print]


Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas.
De Grassi A, Iannelli F, Cereda M, Volorio S, et al.
Genome Biol. 2014 Aug 30;15(8):437.


Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis.
Eckel-Passow JE, Igel DA, Serie DJ, Joseph RW, et al.
Urol Oncol. 2014 Aug 27. [Epub ahead of print]


Mutations in APOPT1, encoding a mitochondrial protein, cause cavitating leukoencephalopathy with cytochrome c oxidase deficiency.
Melchionda L, Haack TB, Hardy S, Abbink TE, et al.
Am J Hum Genet. 2014 Aug 27. [Epub ahead of print]


Identification of actionable mutations in malignant pleural mesothelioma.
Shukuya T, Serizawa M, Watanabe M, Akamatsu H, et al.
Lung Cancer. 2014 Aug 18. [Epub ahead of print]

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.