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Richard Houlston and colleagues report results of a genome-wide association study of childhood acute lymphoblastic leukemia. Identified risk loci include IKZF1 on 7p12.2 and ARID5B on 10q21.2, which encode transcription factors involved in the differentiation of B-cell progenitors.
Marco Tartaglia and colleagues report the identification of mutations of SHOC2 in individuals with Noonan-like syndrome with loose anagen hair. The mutations cause aberrantly acquired N-myristoylation of SHOC2 resulting in aberrant targeting of SHOC2 to the plasma membrane. SHOC2 is believed to function as a scaffold linking RAS to downstream signal transducers.
Mary Relling and colleagues report results of a genome-wide association study of childhood acute lymphoblastic leukemia (ALL) and its subtypes, identifying a specific association between common variants in ARID5B and B-hyperdiploid ALL.
Joseph Gleeson and colleagues show that mutations in INPP5E, encoding the enzyme inositol polyphosphate-5- phosphatase E, cause Joubert syndrome. Functional studies suggest that the mutations promote premature destabilization of cilia in response to stimulation.
Stephane Schurmans and colleagues show that mice lacking the enzyme inositol polyphosphate-5-phosphatase E (Inpp5e) develop a multiorgan disorder with defects in primary cilia. They also report a mutation in human INPP5E in a family with MORM syndrome, a condition similar to Bardet-Biedl syndrome.
Xifeng Wu and colleagues show that a common variant in the prostate stem cell antigen (PSCA) gene on 8q24 is associated with susceptibility to urinary bladder cancer. The risk allele truncates the amino terminus of the PSCA gene product and reduces PSCA promoter activity in bladder cancer cell lines.
Stephen Chanock and colleagues report a genome-wide association study of pancreatic cancer. They identify common variants at the ABO blood group locus associated with susceptibility to pancreatic cancer, consistent with previous epidemiological evidence suggesting that individuals with A or B blood types have greater risk of this cancer than individuals with blood type O.
Paul Pharoah and colleagues report results of the first genome-wide association study for epithelial ovarian cancer. They identify a susceptibility locus on chromosome 9p22.
Stefan Mundlos and colleagues report the identification of mutations in PYCR1 that cause autosomal recessive cutis laxa. PYCR1 encodes an enzyme involved in proline metabolism and localizes to mitochondria.
Gary Felsenfeld and colleagues examine the distribution of H3.3- and H2A.Z-containing nucleosomes genome-wide. They find that regions at transcription start sites of active genes, which were thought to be “nucleosome-free regions,” are enriched for unstable H2A.Z and H3.3 double-variant nucleosomes. These results suggest that double-variant nucleosomes may be important in the regulation of transcription factor access to promoters.
Christine Seidman and colleagues report that 1% of individuals with sporadic non-syndromic tetralogy of Fallot show copy number gains or losses at chromosome 1q21.1. They also report copy number changes at other loci that likely contribute to the etiology of this congenital heart malformation.
Timothy Spector, Mario Falchi and colleagues report a genome-wide association study for development of cutaneous nevi, the strongest known risk factor for cutaneous melanoma. They report two loci associated with nevus count, and show these loci are also associated with susceptibility to melanoma.
Margaret Wrensch and colleagues report a genome-wide association and replication study for high-grade glioma. They show that common variants in the CDKN2B and RTEL1 regions are associated with risk of this aggressive brain tumor.
Simon Stacey and colleagues report several new susceptibility variants for basal cell carcinoma, including coding variants in KRT5, a variant at 9p21 near CDKN2A and CDKN2B and a variant at 7q32 near KLF14. The latter is an imprinted gene, and the effect at this locus is dependent on the parental origin of the risk allele.
Richard Houlston, Melissa Bondy and colleagues identify variants at five loci associated with glioma susceptibility, providing insights into the etiology of this primary brain tumor. The risk loci include common variants near TERT, CDKN2A-CDKN2B and RTEL1.
Timothy Bishop and colleagues from GenoMEL present a genome-wide association study for melanoma. They report three loci associated with susceptibility to melanoma, of which two were previously associated with pigmentation.
Gudmar Thorleifsson and colleagues report a genome-wide association study for kidney stones. They report common variants in CLDN14 associated with increased risk of kidney stone disease.
Klaus Schwarz and colleagues show that mutations affecting the secretory COPII coat component SEC23B cause congenital dyserythropoetic anemia type II, a rare disease marked by defective cytokinesis in erythroblasts and membrane abnormalities in nucleated and peripheral red blood cells.
James Lupski and colleagues provide evidence that a replication-based mechanism termed FoSTeS/MMBIR can mediate rearrangements in humans ranging in size from a few hundred base pairs to several megabases. They propose that FoSTeS/MMBIR could be an important mechanism for generating structural variation.