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In Print: Last Week's Clinical Sequencing Papers of Note: Jun 19, 2013


Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing; applications in tumour subclone resolution.
Stead LF, Sutton KM, Taylor GR, Quirke P, Rabbitts P.
Hum Mutat. 2013 Jun 13. [Epub ahead of print]

Thymoma patients treated in a phase I clinic at MD Anderson Cancer Center: responses to mTOR inhibitors and molecular analyses.
Wheler J, Hong D, Swisher SG, Falchook G, et al.
Oncotarget. 2013 Jun 10. [Epub ahead of print]

Next-generation carrier screening.
Umbarger MA, Kennedy CJ, Saunders P, Breton B, et al.
Genet Med. 2013 Jun 13. [Epub ahead of print]

A modified RNA-seq approach for whole genome sequencing of RNA viruses from faecal and blood samples.
Batty EM, Wong TH, Trebes A, Argoud K, et al.
PLoS One. 2013 Jun 10;8(6):e66129.

Effective noninvasive zygosity determination by maternal plasma target region sequencing.
Zheng J, Xu C, Guo J, Wei Y, et al.
PLoS One. 2013 Jun 10;8(6):e65050.

Discovery of potential new gene variants and inflammatory cytokine associations with fibromyalgia syndrome by whole exome sequencing.
Feng J, Zhang Z, Wu X, Mao A, et al.
PLoS One. 2013 Jun 10;8(6):e65033.

The relative timing of mutations in a breast cancer genome.
Newman S, Howarth KD, Greenman CD, Bignell GR, et al.
PLoS One. 2013 Jun 10;8(6):e64991.

The number of candidate variants in exome sequencing for Mendelian disease under no genetic heterogeneity.
Nishino J, Mano S.
Comput Math Methods Med. 2013;2013:179761.

Comparing somatic mutation-callers: beyond Venn diagrams.
Kim SY, Speed TP.
BMC Bioinformatics. 2013 Jun 10;14(1):189.

Mutations in COQ2 in familial and sporadic multiple-system atrophy.
The Multiple-System Atrophy Research Collaboration.
N Engl J Med. 2013 Jun 12. [Epub ahead of print]

Joint genotype inference with germline and somatic mutations.
Bareke E, Saillour V, Spinella JF, Vidal R, et al.
BMC Bioinformatics. 2013;14 Suppl 5:S3.

Isolation and high-throughput sequencing of two-closely linked epistatic hypertension susceptibility loci with a panel of bicongenic strains.
Pillai R, Waghulde H, Nie Y, Gopalakrishnan K, et al.
Physiol Genomics. 2013 Jun 11. [Epub ahead of print]

Comprehensive genomic profiling in diabetic nephropathy reveals the predominance of pro-inflammatory pathways.
Kelly KJ, Liu Y, Zhang J, Goswami C, et al.
Physiol Genomics. 2013 Jun 11. [Epub ahead of print]

AP1S2 is mutated in X-linked Dandy-Walker malformation with intellectual disability, basal ganglia disease and seizures (Pettigrew syndrome).
Cacciagli P, Desvignes JP, Girard N, Delepine M, et al.
Eur J Hum Genet. 2013 Jun 12. [Epub ahead of print]

Targeted next-generation sequencing as a comprehensive test for patients with and female carriers of DMD/BMD: a multi-population diagnostic study.
Wei X, Dai Y, Yu P, Qu N, et al.
Eur J Hum Genet. 2013 Jun 12. [Epub ahead of print]

AKAPs integrate genetic findings for autism spectrum disorders.
Poelmans G, Franke B, Pauls DL, Glennon JC, Buitelaar JK.
Transl Psychiatry. 2013 Jun 11;3:e270.

Whole-exome sequencing enables rapid determination of xeroderma pigmentosum molecular etiology.
Ortega-Recalde O, Vergara JI, Fonseca DJ, Ríos X, et al.
PLoS One. 2013 Jun 3;8(6):e64692.

Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets.
Grarup N, Sulem P, Sandholt CH, Thorleifsson G, et al.
PLoS Genet. 2013 Jun;9(6):e1003530.

Global DNA hypermethylation in down syndrome placenta.
Jin S, Lee YK, Lim YC, Zheng Z, et al.
PLoS Genet. 2013 Jun;9(6):e1003515.

Whole exome sequencing identifies mutation of EDNRA involved in ACTH-independent macronodular adrenal hyperplasia.
Zhu J, Cui L, Wang W, Hang XY, et al.
Fam Cancer. 2013 Jun 11. [Epub ahead of print]

Germline SDHA mutation detected by next-generation sequencing in a young index patient with large paraganglioma.
Welander J, Garvin S, Bohnmark R, Isaksson L, et al.
J Clin Endocrinol Metab. 2013 Jun 7. [Epub ahead of print]

Recessive truncating NALCN mutation in infantile neuroaxonal dystrophy with facial dysmorphism.
Köroglu C, Seven M, Tolun A.
J Med Genet. 2013 Jun 7. [Epub ahead of print]

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data.
Larson NB, Fridley BL.
Bioinformatics. 2013 Jun 14. [Epub ahead of print]

SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3.
Nakhro K, Park JM, Hong YB, Park JH, et al.
Neurology. 2013 Jun 7. [Epub ahead of print]

Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing.
Wagner J, Maksimovic J, Farries G, Sim WH, et al.
Inflamm Bowel Dis. 2013 Jun 6. [Epub ahead of print]

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.
Liu C, Yang X, Duffy B, Mohanakumar T, et al.
Nucleic Acids Res. 2013 Jun 8. [Epub ahead of print]

De novo mutations in the genome organizer CTCF cause intellectual disability.
Gregor A, Oti M, Kouwenhoven EN, Hoyer J, et al.
Am J Hum Genet. 2013 Jun 4. [Epub ahead of print]

Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy.
Ravenscroft G, Miyatake S, Lehtokari VL, Todd EJ, et al.
Am J Hum Genet. 2013 Jun 4. [Epub ahead of print]

Long runs of homozygosity are enriched for deleterious variation.
Szpiech ZA, Xu J, Pemberton TJ, Peng W, et al.
Am J Hum Genet. 2013 Jun 4. [Epub ahead of print]

Mutations in RAB28, encoding a farnesylated small GTPase, are associated with autosomal-recessive cone-rod dystrophy.
Roosing S, Rohrschneider K, Beryozkin A, Sharon D, et al.
Am J Hum Genet. 2013 Jun 4. [Epub ahead of print]

NDUFA4 mutations underlie dysfunction of a cytochrome c oxidase subunit linked to human neurological disease.
Pitceathly RD, Rahman S, Wedatilake Y, Polke JM, et al.
Cell Rep. 2013 Jun 5. [Epub ahead of print]

Longitudinal ultra-deep characterization of HIV-1 R5 and X4 subpopulations in patients followed from primary infection to coreceptor switch.
Hedskog C, Brodin J, Heddini A, Bratt G, et al.
AIDS Res Hum Retroviruses. 2013 Jun 7. [Epub ahead of print]