Comput Biol Chem - Rare variants analysis by risk-based variable-threshold method.

Tópicos

{ risk(3053) factor(974) diseas(938) }
{ method(1219) similar(1157) match(930) }
{ general(901) number(790) one(736) }
{ gene(2352) biolog(1181) express(1162) }
{ detect(2391) sensit(1101) algorithm(908) }
{ method(1557) propos(1049) approach(1037) }
{ analysi(2126) use(1163) compon(1037) }
{ problem(2511) optim(1539) algorithm(950) }
{ data(2317) use(1299) case(1017) }
{ sampl(1606) size(1419) use(1276) }
{ howev(809) still(633) remain(590) }
{ intervent(3218) particip(2042) group(1664) }
{ high(1669) rate(1365) level(1280) }
{ sequenc(1873) structur(1644) protein(1328) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ concept(1167) ontolog(924) domain(897) }
{ model(2220) cell(1177) simul(1124) }
{ featur(1941) imag(1645) propos(1176) }
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{ spatial(1525) area(1432) region(1030) }
{ state(1844) use(1261) util(961) }
{ age(1611) year(1155) adult(843) }
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{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
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{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Genome-wide association studies, as a powerful approach for detecting common variants associated with diseases, have revealed many disease-associated loci. However, the traditional association analysis methods do not have enough power for detecting the effects of rare variants with limited sample size. As a solution to this problem, pooling rare variants by their functions into a composite variant provides an alternative way for identifying susceptible genes. In this paper, we propose a new pooling method to test the variant-disease association and to identify the functional rare variants related with the disease. Variants with smaller and larger risk measures defined as the ratio of allele frequencies between cases and controls are pooled and a chi-square test of the resultant pooled table is calculated. We vary the threshold of pooling over all possible values and use the maximal chi-square as test statistic. The maximal chi-square is in fact the global maximum over all possible poolings. Our approach is similar to the existing variable-threshold method, but we threshold on the risk measure instead of allele frequencies of controls. Simulation results show that our method performs better in both association testing and variant selection.

Resumo Limpo

genomewid associ studi power approach detect common variant associ diseas reveal mani diseaseassoci loci howev tradit associ analysi method enough power detect effect rare variant limit sampl size solut problem pool rare variant function composit variant provid altern way identifi suscept gene paper propos new pool method test variantdiseas associ identifi function rare variant relat diseas variant smaller larger risk measur defin ratio allel frequenc case control pool chisquar test result pool tabl calcul vari threshold pool possibl valu use maxim chisquar test statist maxim chisquar fact global maximum possibl pool approach similar exist variablethreshold method threshold risk measur instead allel frequenc control simul result show method perform better associ test variant select

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