Abstract：
:The central challenges in tumor sequencing studies is to identify driver genes and pathways, investigate their functional relationships, and nominate drug targets. The efficiency of these analyses, particularly for infrequently mutated genes, is compromised when subjects carry different combinations of driver mutations. Mutual exclusivity analysis helps address these challenges. To identify mutually exclusive gene sets (MEGS), we developed a powerful and flexible analytic framework based on a likelihood ratio test and a model selection procedure. Extensive simulations demonstrated that our method outperformed existing methods for both statistical power and the capability of identifying the exact MEGS, particularly for highly imbalanced MEGS. Our method can be used for de novo discovery, for pathway-guided searches, or for expanding established small MEGS. We applied our method to the whole-exome sequencing data for 13 cancer types from The Cancer Genome Atlas (TCGA). We identified multiple previously unreported non-pairwise MEGS in multiple cancer types. For acute myeloid leukemia, we identified a MEGS with five genes (FLT3, IDH2, NRAS, KIT, and TP53) and a MEGS (NPM1, TP53, and RUNX1) whose mutation status was strongly associated with survival (p = 6.7 × 10(-4)). For breast cancer, we identified a significant MEGS consisting of TP53 and four infrequently mutated genes (ARID1A, AKT1, MED23, and TBL1XR1), providing support for their role as cancer drivers.
journal_name
Am J Hum Genetjournal_title
American journal of human geneticsauthors
Hua X,Hyland PL,Huang J,Song L,Zhu B,Caporaso NE,Landi MT,Chatterjee N,Shi Jdoi
10.1016/j.ajhg.2015.12.021subject
Has Abstractpub_date
2016-03-03 00:00:00pages
442-455issue
3eissn
0002-9297issn
1537-6605pii
S0002-9297(16)00002-1journal_volume
98pub_type
杂志文章abstract：:Electrophoretic and quantitative studies reveal that 85% of Japanese carry an atypical liver alcohol dehydrogenase (ADH). The frequency of ADH polymorphism is identical with the reported frequency of alcohol sensitivity in the Japanese population. This identity in population frequencies points to a causative relations...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1975-11-01 00:00:00
abstract：:Diffuse panbronchiolitis affecting East Asians is strongly associated with the class I human leukocyte antigen (HLA) alleles. Recent observations suggest that a major disease-susceptibility gene may be located between the HLA-B and HLA-A loci in the class I region of the major histocompatibility complex on chromosome ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302786
更新日期：2000-02-01 00:00:00
abstract：:An autosomal recessive deficiency of acid alpha-glucosidase (GAA), type II glycogenosis, is genetically and clinically heterogeneous. The discovery of an enzyme-inactivating genomic deletion of exon 18 in three unrelated genetic compound patients--two infants and an adult--provided a rare opportunity to analyze the ef...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1995-04-01 00:00:00
abstract：:Attention-deficit hyperactivity disorder (ADHD) affects approximately 3%-5% of children in the United States. In the current psychiatric nomenclature, ADHD comprises three subtypes: inattentive, hyperactive-impulsive, and combined. In this study, we used four analytic strategies to examine the association and linkage ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302132
更新日期：1998-12-01 00:00:00
abstract：:In Williams syndrome (WS), a deletion of approximately 1.5 Mb on one copy of chromosome 7 causes specific physical, cognitive, and behavioral abnormalities. Molecular dissection of the phenotype may be a route to identification of genes important in human cognition and behavior. Among the genes known to be deleted in ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302214
更新日期：1999-01-01 00:00:00
abstract：:Waardenburg syndrome type 4 (WS4), also called Shah-Waardenburg syndrome, is a rare neurocristopathy that results from the absence of melanocytes and intrinsic ganglion cells of the terminal hindgut. WS4 is inherited as an autosomal recessive trait attributable to EDN3 or EDNRB mutations. It is inherited as an autosom...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302895
更新日期：2000-05-01 00:00:00
abstract：:Aplastic anemia (AA) and myelodysplasia (MDS) are forms of bone marrow failure that are often part of the same progressive underlying disorder. While most cases are simplex and idiopathic, some show a clear pattern of inheritance; therefore, elucidating the underlying genetic cause could lead to a greater understandin...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2012.03.020
更新日期：2012-05-04 00:00:00
abstract：:Analysis of human-Chinese hamster somatic cell hybrids with spontaneously derived chromosome structural changes has provided data for the regional and subregional localization of gene loci which have previously been assigned to human chromosomes 2, 12, and X. Correlation of the expression of human gene loci with the h...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1975-09-01 00:00:00
abstract：:Regions on chromosomes 7 and 19 were recently reported to contain susceptibility loci that regulate tumor aggressiveness of prostate cancer. To confirm these findings, we analyzed genome scan data from 161 pedigrees affected with prostate cancer. Using the Gleason score as a quantitative measure of tumor aggressivenes...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/368230
更新日期：2003-03-01 00:00:00
abstract：:In studying the relationship between genetic abnormalities of red blood cells and malaria endemicity in the Vanuatu archipelago in the southwestern Pacific, we have found that of 1,442 males tested, 98 (6.8%) were G6PD deficient. The prevalence of GdPD deficiency varied widely (0%-39%), both from one island to another...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1995-01-01 00:00:00
abstract：:Cisplatin, a platinating agent commonly used to treat several cancers, is associated with nephrotoxicity, neurotoxicity, and ototoxicity, which has hindered its utility. To gain a better understanding of the genetic variants associated with cisplatin-induced toxicity, we present a stepwise approach integrating genotyp...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/519850
更新日期：2007-09-01 00:00:00
abstract：:Hermansky-Pudlak syndrome (HPS) is genetically heterogeneous, and mutations in seven genes have been reported to cause HPS. Autozygosity mapping studies were undertaken in a large consanguineous family with HPS. Affected individuals displayed features of incomplete oculocutaneous albinism and platelet dysfunction. Ski...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/499338
更新日期：2006-01-01 00:00:00
abstract：:Mucopolysaccharidosis type I (MPS-I) is an autosomal recessive genetic disease caused by a deficiency of the lysosomal glycosidase alpha-L-iduronidase. Hurler (severe), Scheie (mild), and Hurler/Scheie (intermediate) syndromes are clinical subtypes of MPS-I, but it is difficult to distinguish between these subtypes by...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1993-11-01 00:00:00
abstract：:The affected sib-pair method has been used to investigate the mode of inheritance, and to estimate the "disease" allele frequency, for a number of HLA-associated diseases. One of the assumptions of the original sib-pair method is that the disease confers no selective disadvantage on affected individuals. This is obvio...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1984-03-01 00:00:00
abstract：:A novel type IV collagen, alpha 3(IV), has recently been identified in human and bovine basement membranes. Here we describe the cloning and sequencing of a cDNA encoding 218 residues of the NC1 domain of the human alpha 3(IV) chain. Of interest is the possible role of abnormalities of the alpha 3(IV) chain in Alport ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1991-09-01 00:00:00
abstract：:The power of structured exploratory data analysis (SEDA) to discriminate among major genic, polygenic, and nongenetic determination of phenotypes was investigated using computer simulation. Three classes of SEDA indices (the major gene index, the offspring between parents function, and the midparent-child correlation ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1984-01-01 00:00:00
abstract：:Intracytoplasmic sperm injection (ICSI) has been used in combination with testicular sperm extraction to achieve pregnancies in couples with severe male-factor infertility, yet many of the underlying genetic mechanisms remain largely unknown. To investigate nondisjunction in mitotic and meiotic germ cells, we performe...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302402
更新日期：1999-06-01 00:00:00
abstract：:Each year at the annual meeting of The American Society of Human Genetics (ASHG), addresses are given in honor of the Society and a number of award winners. A summary of each of these is provided below. On the following pages, we have printed the Presidential Address as well as the addresses for the William Allan Awar...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2019.02.019
更新日期：2019-03-07 00:00:00
abstract：:We have analyzed 247 Brazilian mtDNAs for hypervariable segment (HVS)-I and selected restriction fragment-length-polymorphism sites, to assess their ancestry in different continents. The total sample showed nearly equal amounts of Native American, African, and European matrilineal genetic contribution but with regiona...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/303004
更新日期：2000-08-01 00:00:00
abstract：:Colorectal cancer (CRC) heritability has been estimated to be around 30%. However, mutations in the known CRC-susceptibility genes explain CRC risk in fewer than 10% of affected individuals. Germline mutations in DNA-repair genes (DRGs) have recently been reported in CRC, but their contribution to CRC risk is largely ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2018.01.018
更新日期：2018-03-01 00:00:00
abstract：:Previously, we demonstrated evidence of linkage to bipolar affective disorder (BP) in a single large, multigenerational family with a LOD score of 3.41 at the PFKL locus on chromosome 21q22.3. Additional families showed little support for linkage to PFKL under homogeneity or heterogeneity, in that study. We have expan...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302185
更新日期：1999-01-01 00:00:00
abstract：:Genetic hemochromatosis (GH) is believed to be a disease restricted to those of European ancestry. In northwestern Europe, >80% of GH patients are homozygous for one mutation, the substitution of tyrosine for cysteine at position 282 (C282Y) in the unprocessed protein. In a proportion of GH patients, two mutations are...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302318
更新日期：1999-04-01 00:00:00
abstract：:We recently reported the absence of significant linkage of phonological coding dyslexia (PCD) to chromosome 6p23-p21.3 in 79 families with at least two affected siblings, even though linkage of dyslexia to this region has been found in four other independent studies. Whereas, in our previous analyses, we used a qualit...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302764
更新日期：2000-02-01 00:00:00
abstract：:Argininosuccinate lyase (AS lyase) deficiency is an inborn error of the urea cycle with extensive clinical and genetic heterogeneity. We investigated the biochemical basis of the enzyme defect and the genetic heterogeneity in this disorder using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1986-07-01 00:00:00
abstract：:DNA sequence polymorphisms have been used to determine the linear order and recombinational distances separating the Harvey ras 1 oncogene (c-Ha-ras-1), beta-globin, insulin, and parathyroid hormone genes on the short arm of human chromosome 11. Our results indicate that c-Ha-ras-1 is closely linked to both the beta-g...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1984-03-01 00:00:00
abstract：:A patients with seizures, Von Willebrand disease, and symptoms of Turner syndrome was a chromosomal mosaic. In blood culture (1974), 56% of the cells were 45, X 33% 46, XXp+ and 11% 47,XXp + Xp +; in the skin, no cells with 47 chromosomes were found. Presumably the Xp + chromosome arose through a break in the Q-banded...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1977-01-01 00:00:00
abstract：:Our previous studies have revealed a higher frequency of nonpolymorphic electrophoretic variants in blood samples from Amerindians than in similar samples from Caucasians and Japanese. Our present study finds, by contrast, that the frequency of deficiency variants of 11 erythrocyte enzymes, sampled in nine Amerindian ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1984-05-01 00:00:00
abstract：:Adolescent idiopathic scoliosis (AIS) is one of the most common orthopedic disorders, affecting up to 4% of schoolchildren worldwide. We studied seven unrelated multiplex families of southern Chinese descent with AIS, consisting of 25 affected members. A genomewide scan with >400 fluorescent microsatellite markers was...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/341607
更新日期：2002-08-01 00:00:00
abstract：:Autosomal dominant familial exudative vitreoretinopathy (adFEVR) is a hereditary disorder characterized by the incomplete vascularization of the peripheral retina. The primary biochemical defect in adFEVR is unknown. The adFEVR locus has tentatively been assigned to 11q by linkage studies. We report the results of an ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1992-10-01 00:00:00
abstract：:Now that the cystic fibrosis (CF) gene has been identified, direct genetic testing for this disorder is available. The current lack of precision has generated a controversy concerning whether population screening is advisable. However, there is general agreement that testing for CF carriers should be offered to CF-aff...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1995-08-01 00:00:00
