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In Print: Last Week's Clinical Sequencing Papers of Note: May 22, 2013


Evaluation of autosomal dominant retinal dystrophy genes in an unaffected cohort suggests rare or private missense variants may often be benign.
Strom SP, Gorin MB.
Mol Vis. 2013 May 6;19:980-985.

LMX1B mutations cause hereditary FSGS without extrarenal involvement.
Boyer O, Woerner S, Yang F, Oakeley EJ, et al.
J Am Soc Nephrol. 2013 May 16. [Epub ahead of print]

Disruption of TBC1D7, a subunit of the TSC1-TSC2 protein complex, in intellectual disability and megalencephaly.
Capo-Chichi JM, Tcherkezian J, Hamdan FF, Décarie JC, et al.
J Med Genet. 2013 May 17. [Epub ahead of print]

Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR.
Trujillano D, Ramos MD, González J, Tornador C, et al.
J Med Genet. 2013 May 17. [Epub ahead of print]

Loss of function of the E3 ubiquitin-protein ligase UBE3B causes Kaufman oculocerebrofacial syndrome.
Flex E, Ciolfi A, Caputo V, Fodale V, et al.
J Med Genet. 2013 May 17. [Epub ahead of print]

Mutations in TNK2 in severe autosomal recessive infantile-onset epilepsy.
Hitomi Y, Heinzen EL, Donatello S, Dahl HH, et al.
Ann Neurol. 2013 May 20. [Epub ahead of print]

Fetal aneuploidy detection by maternal plasma DNA sequencing: a technology assessment.
Walsh JM, Goldberg JD.
Prenat Diagn. 2013 Jun;33(6):514-520.

Significance of expression of ITGA5 and its splice variants in acute myeloid leukemia: A report from the Children's Oncology Group.
Walter RB, Laszlo GS, Alonzo TA, Gerbing RB, et al.
Am J Hematol. 2013 May 20. [Epub ahead of print]

Unique X-linked familial FSGS with co-segregating heart block disorder is associated with a mutation in the NXF5 gene.
Esposito T, Lea RA, Maher BH, Moses D, et al.
Hum Mol Genet. 2013 May 16. [Epub ahead of print]

Germline BAP1 mutations predispose to renal cell carcinomas.
Popova T, Hebert L, Jacquemin V, Gad S, et al.
Am J Hum Genet. 2013 May 14. [Epub ahead of print]

Mutations in POFUT1, encoding protein O-fucosyltransferase 1, cause generalized Dowling-Degos disease.
Li M, Cheng R, Liang J, Yan H, et al.
Am J Hum Genet. 2013 May 14. [Epub ahead of print]

Sequence kernel association tests for the combined effect of rare and common variants.
Ionita-Laza I, Lee S, Makarov V, Buxbaum JD, Lin X.
Am J Hum Genet. 2013 May 14. [Epub ahead of print]

Massively parallel sequencing reveals maternal somatic IL2RG mosaicism in an X-linked severe combined immunodeficiency family.
Alsina L, González-Roca E, Giner MT, Piquer M, et al.
J Allergy Clin Immunol. 2013 May 15. [Epub ahead of print]

WDR19: A retrograde intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa (arRP) and in Senior Loken syndrome (SLS).
Coussa RG, Otto EA, Gee HY, Arthurs P, et al.
Clin Genet. 2013 May 17. [Epub ahead of print]

The use of next-generation sequencing in clinical diagnosis of familial hypercholesterolemia.
Vandrovcova J, Thomas ER, Atanur SS, Norsworthy PJ, et al.
Genet Med. 2013 May 16. [Epub ahead of print]

Robustness of amplicon deep sequencing underlines its utility in clinical applications.
Grossmann V, Roller A, Klein HU, Weissmann S, et al.
J Mol Diagn. 2013 May 13. [Epub ahead of print]

A combination of mutations in AKR1D1 and SKIV2L in a family with severe infantile liver disease.
Morgan NV, Hartley JL, Setchell KD, Simpson MA, et al.
Orphanet J Rare Dis. 2013 May 16;8(1):74.

Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint.
McGovern RA, Symons J, Poon AF, Harrigan PR, et al.
J Antimicrob Chemother. 2013 May 14. [Epub ahead of print]

Exome sequencing and systems biology converge to identify novel mutations in the L-type calcium channel, CACNA1C, linked to autosomal dominant Long QT syndrome.
Boczek NJ, Best JM, Tester DJ, Giudicessi JR, et al.
Circ Cardiovasc Genet. 2013 May 15. [Epub ahead of print]

Exome sequencing as a diagnostic tool to identify a causal mutation in genetically highly heterogeneous limb-girdle muscular dystrophy.
Matsuura T, Kurosaki T, Omote Y, Minami N, et al.
J Hum Genet. 2013 May 16. [Epub ahead of print]

Whole-genome sequencing in health care.
van El CG, Cornel MC, Borry P, Hastings RJ, et al.
Eur J Hum Genet. 2013 Jun;21(6):580-4.

The genomic landscape of small intestine neuroendocrine tumors.
Banck MS, Kanwar R, Kulkarni AA, Boora GK, et al.
J Clin Invest. 2013 May 15. [Epub ahead of print]

Mutations in extracellular matrix genes NID1 and LAMC1 cause autosomal dominant Dandy-Walker malformation and occipital cephaloceles.
Darbro BW, Mahajan VB, Gakhar L, Skeie JM, et al.
Hum Mutat. 2013 May 14. [Epub ahead of print]

Expanding the phenotype of IQSEC2 mutations: truncating mutations in severe intellectual disability.
Tran Mau-Them F, Willems M, Albrecht B, Sanchez E, et al.
Eur J Hum Genet. 2013 May 15. [Epub ahead of print]

Autonomy and the patient's right 'not to know' in clinical whole-genomic sequencing.
Townsend A, Rousseau F, Friedman J, Adam S, et al.
Eur J Hum Genet. 2013 May 15. [Epub ahead of print]

Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease.
Wang J, Qi J, Zhao H, He S, et al.
Sci Rep. 2013 May 15;3:1843.

Next-generation sequencing identifies transportin 3 as the causative gene for LGMD1F.
Torella A, Fanin M, Mutarelli M, Peterle E, et al.
PLoS One. 2013 May 7;8(5):e63536.

A comprehensive next generation sequencing based genetic testing strategy to improve diagnosis of inherited pheochromocytoma and paraganglioma.
Rattenberry E, Vialard L, Yeung A, Bair H, et al.
J Clin Endocrinol Metab. 2013 May 10. [Epub ahead of print]

Protein kinase C δ deficiency causes mendelian systemic lupus erythematosus with B-cell defective apoptosis and hyperproliferation.
Belot A, Kasher PR, Trotter EW, Foray AP, et al.
Arthritis Rheum. 2013 May 10. [Epub ahead of print]

Whole-exome sequencing identifies ADAM10 mutations as a cause of reticulate acropigmentation of Kitamura, a clinical entity distinct from Dowling-Degos disease.
Kono M, Sugiura K, Suganuma M, Hayashi M, et al.
Hum Mol Genet. 2013 May 10. [Epub ahead of print]

De novo mutations in histone-modifying genes in congenital heart disease.
Zaidi S, Choi M, Wakimoto H, Ma L, et al.
Nature. 2013 May 12. [Epub ahead of print]

Identification of a Ninein (NIN) mutation in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype.
Grosch M, Grüner B, Spranger S, Stütz AM, et al.
Matrix Biol. 2013 May 9. [Epub ahead of print]

The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders.
Dames S, Chou LS, Xiao Y, Wayman T, et al.
J Mol Diagn. 2013 May 8. [Epub ahead of print]

Exome sequencing released a case of X-linked adrenoleukodystrophy mimicking recessive hereditary spastic paraplegia.
Zhan ZX, Liao XX, Du J, Luo YY, et al.
Eur J Med Genet. 2013 May 8. [Epub ahead of print]

Cenani-Lenz syndrome restricted to limb and kidney anomalies associated with a novel LRP4 missense mutation.
Khan T N, J K, A Z, F K, et al.
Eur J Med Genet. 2013 May 7. [Epub ahead of print]

Molecular defects in the motor adaptor BICD2 cause proximal spinal muscular atrophy with autosomal-dominant inheritance.
Peeters K, Litvinenko I, Asselbergh B, Almeida-Souza L, et al.
Am J Hum Genet. 2013 May 7. [Epub ahead of print]

Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders.
Nakajima M, Mizumoto S, Miyake N, Kogawa R, et al.
Am J Hum Genet. 2013 May 7. [Epub ahead of print]

Mutations in BICD2, which encodes a Golgin and important motor adaptor, cause congenital autosomal-dominant spinal muscular atrophy.
Neveling K, Martinez-Carrera LA, Hölker I, Heister A, et al.
Am J Hum Genet. 2013 May 7. [Epub ahead of print]

Diverse mechanisms of somatic structural variations in human cancer genomes.
Yang L, Luquette LJ, Gehlenborg N, Xi R, et al.
Protopopov Cell. 2013 May 9;153(4):919-29.

Targeted capture and sequencing for detection of mutations causing early onset epileptic encephalopathy.
Kodera H, Kato M, Nord AS, Walsh T, et al.
Epilepsia. 2013 May 10. [Epub ahead of print]

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.