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A framework for constructing de Bruijn sequences via simple successor rules
Gabric, Daniel,Sawada, Joe,Williams, Aaron,Wong, Dennis Elsevier 2018 Discrete mathematics Vol.341 No.11
<P><B>Abstract</B></P> <P>We present a simple framework for constructing de Bruijn sequences, and more generally, universal cycles, via successor rules. The framework is based on the often used method of joining disjoint cycles. It generalizes four previously known de Bruijn sequence constructions and is applied to derive three new and simple de Bruijn sequence constructions. Four of the constructions apply the pure cycling register and three apply the complemented cycling register. The correctness of each new construction is easily proved using the new framework. Each of the three new de Bruijn sequence constructions can be generated in O ( n ) -time per bit using O ( n ) -space.</P>
The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers
Amos, Christopher I.,Dennis, Joe,Wang, Zhaoming,Byun, Jinyoung,Schumacher, Fredrick R.,Gayther, Simon A.,Casey, Graham,Hunter, David J.,Sellers, Thomas A.,Gruber, Stephen B.,Dunning, Alison M.,Michail American Association for Cancer Research 2017 Cancer epidemiology, biomarkers & prevention Vol.26 No.1
<P>Impact: Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. (C)2016 AACR.</P>
Constructing de Bruijn sequences with co-lexicographic order: The k -ary Grandmama sequence
Dragon, Patrick Baxter,Hernandez, Oscar I.,Sawada, Joe,Williams, Aaron,Wong, Dennis Elsevier 2018 European journal of combinatorics : Journal europ& Vol.72 No.-
<P><B>Abstract</B></P> <P>A k -ary de Bruijn sequence of order n is a circular k -ary string of length <SUP> k n </SUP> which contains every k -ary string of length n exactly once as a substring. It is well-known that a k -ary de Bruijn sequence of order n can be constructed by concatenating the aperiodic prefixes of the k -ary necklaces of length n in lexicographic order. In this article we prove that an alternate de Bruijn sequence is created by replacing lexicographic order with co-lexicographic order. We also provide a simple successor rule for generating each successive symbol in O ( n ) -time.</P>
Association analysis identifies 65 new breast cancer risk loci
Michailidou, Kyriaki,Lindströ,m, Sara,Dennis, Joe,Beesley, Jonathan,Hui, Shirley,Kar, Siddhartha,Lemaç,on, Audrey,Soucy, Penny,Glubb, Dylan,Rostamianfar, Asha,Bolla, Manjeet K.,Wang, Qin,Tyr Macmillan Publishers Limited, part of Springer Nat 2017 Nature Vol.551 No.7678
<P>Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry(1). We identified 65 new loci that are associated with overall breast cancer risk at P < 5 x 10(-8). The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.</P>
Michailidou, Kyriaki,Beesley, Jonathan,Lindstrom, Sara,Canisius, Sander,Dennis, Joe,Lush, Michael J,Maranian, Mel J,Bolla, Manjeet K,Wang, Qin,Shah, Mitul,Perkins, Barbara J,Czene, Kamila,Eriksson, Mi Nature Publishing Group, a division of Macmillan P 2015 Nature genetics Vol.47 No.4
Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P < 5 × 10<SUP>−8</SUP>. Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid substitution encoded in EXO1.
Zheng, Wei,Zhang, Ben,Cai, Qiuyin,Sung, Hyuna,Michailidou, Kyriaki,Shi, Jiajun,Choi, Ji-Yeob,Long, Jirong,Dennis, Joe,Humphreys, Manjeet K.,Wang, Qin,Lu, Wei,Gao, Yu-Tang,Li, Chun,Cai, Hui,Park, Sue K Oxford University Press 2013 Human Molecular Genetics Vol.22 No.12
<P>In a consortium including 23 637 breast cancer patients and 25 579 controls of East Asian ancestry, we investigated 70 single-nucleotide polymorphisms (SNPs) in 67 independent breast cancer susceptibility loci recently identified by genome-wide association studies (GWASs) conducted primarily in European-ancestry populations. SNPs in 31 loci showed an association with breast cancer risk at <I>P</I> < 0.05 in a direction consistent with that reported previously. Twenty-one of them remained statistically significant after adjusting for multiple comparisons with the Bonferroni-corrected significance level of <0.0015. Eight of the 70 SNPs showed a significantly different association with breast cancer risk by estrogen receptor (ER) status at <I>P</I> < 0.05. With the exception of rs2046210 at 6q25.1, the seven other SNPs showed a stronger association with ER-positive than ER-negative cancer. This study replicated all five genetic risk variants initially identified in Asians and provided evidence for associations of breast cancer risk in the East Asian population with nearly half of the genetic risk variants initially reported in GWASs conducted in European descendants. Taken together, these common genetic risk variants explain ∼10% of excess familial risk of breast cancer in Asian populations.</P>
Genome-wide association analysis identifies three new breast cancer susceptibility loci
Ghoussaini, Maya,Fletcher, Olivia,Michailidou, Kyriaki,Turnbull, Clare,Schmidt, Marjanka K,Dicks, Ed,Dennis, Joe,Wang, Qin,Humphreys, Manjeet K,Luccarini, Craig,Baynes, Caroline,Conroy, Don,Maranian, Nature Publishing Group, a division of Macmillan P 2012 Nature genetics Vol.44 No.3
Breast cancer is the most common cancer among women. To date, 22 common breast cancer susceptibility loci have been identified accounting for ??% of the heritability of the disease. We attempted to replicate 72 promising associations from two independent genome-wide association studies (GWAS) in ??0,000 cases and ??8,000 controls from 41 case-control studies and 9 breast cancer GWAS. We identified three new breast cancer risk loci at 12p11 (rs10771399; P = 2.7 ? 10<SUP>??35</SUP>), 12q24 (rs1292011; P = 4.3 ? 10<SUP>??19</SUP>) and 21q21 (rs2823093; P = 1.1 ? 10<SUP>??12</SUP>). rs10771399 was associated with similar relative risks for both estrogen receptor (ER)-negative and ER-positive breast cancer, whereas the other two loci were associated only with ER-positive disease. Two of the loci lie in regions that contain strong plausible candidate genes: PTHLH (12p11) has a crucial role in mammary gland development and the establishment of bone metastasis in breast cancer, and NRIP1 (21q21) encodes an ER cofactor and has a role in the regulation of breast cancer cell growth.
Han, Mi-Ryung,Zheng, Wei,Cai, Qiuyin,Gao, Yu-Tang,Zheng, Ying,Bolla, Manjeet K.,Michailidou, Kyriaki,Dennis, Joe,Wang, Qin,Dunning, Alison M.,Brennan, Paul,Chen, Shou-Tung,Choi, Ji-Yeob,Hartman, Mikae Oxford University Press 2017 Carcinogenesis Vol.38 No.5
<P>Over the past 20 years, high-penetrance pathogenic mutations in genes BRCA1, BRCA2, TP53, PTEN, STK11 and CDH1 and moderate-penetrance mutations in genes CHEK2, ATM, BRIP1, PALB2, RAD51C, RAD50 and NBN have been identified for breast cancer. In this study, we investigated whether there are additional variants in these 13 genes associated with breast cancer among women of Asian ancestry. We analyzed up to 654 single nucleotide polymorphisms (SNPs) from 6269 cases and 6624 controls of Asian descent included in the Breast Cancer Association Consortium (BCAC), and up to 236 SNPs from 5794 cases and 5529 controls included in the Shanghai Breast Cancer Genetics Study (SBCGS). We found three missense variants with minor allele frequency (MAF) < 0.05: rs80358978 (Gly2508Ser), rs80359065 (Lys2729Asn) and rs11571653 (Met784Val) in the BRCA2 gene, showing statistically significant associations with breast cancer risk, with P-values of 1.2 x 10(-4), 1.0 x 10(-3) and 5.0 x 10(-3), respectively. In addition, we found four low-frequency variants (rs8176085, rs799923, rs8176173 and rs8176258) in the BRCA1 gene, one common variant in the CHEK2 gene (rs9620817), and one common variant in the PALB2 gene (rs13330119) associated with breast cancer risk at P < 0.01. Our study identified several new risk variants in BRCA1, BRCA2, CHEK2, and PALB2 genes in relation to breast cancer risk in Asian women. These results provide further insights that, in addition to the high/moderate penetrance mutations, other low-penetrance variants in these genes may also contribute to breast cancer risk.</P>
Rudolph, Anja,Song, Minsun,Brook, Mark N,Milne, Roger L,Mavaddat, Nasim,Michailidou, Kyriaki,Bolla, Manjeet K,Wang, Qin,Dennis, Joe,Wilcox, Amber N,Hopper, John L,Southey, Melissa C,Keeman, Renske,Fas Oxford University Press 2018 International journal of epidemiology Vol.47 No.2
<P>Conclusions: The combined effects of the 77-SNP PRS and environmental risk factors for breast cancer are generally well described by a multiplicative model. Larger studies are required to confirm possible departures from the multiplicative model for individual risk factors, and assess models specific for ER-negative disease.</P>
Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer
Phelan, Catherine M,Kuchenbaecker, Karoline B,Tyrer, Jonathan P,Kar, Siddhartha P,Lawrenson, Kate,Winham, Stacey J,Dennis, Joe,Pirie, Ailith,Riggan, Marjorie J,Chornokur, Ganna,Earp, Madalene A,Lyra J Nature Pub. Co 2017 Nature genetics Vol.49 No.5
<P>To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC.</P>