Determination of sibship in any two persons

Wenk, Robert E.; Traver, M; Chiafari, Francis A.

doi:10.1046/j.1537-2995.1996.36396182146.x

Cited by 64 publications

(79 citation statements)

References 3 publications

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“…Statistical analysis was performed using Instat (Graph Pad Software, San Diego, CA), Prism (Graph Pad Software), PHASE version 2.1 [26,55], DnaSP 3.5 (http://www.bio.ub.es/julio/DnaSP.html), Microsoft Excel (Microsoft Corporation, Redmond, WA) and Haploview 3.32 (wwwbroad.mit.edu/mpg/haploview) [21] First degree relatives were identified by calculating cumulative sibship indices (CSIs) using a preliminary C11 analysis software (under development by Cobb and Taylor) and the STR allele data for the entire study population with frequencies provided with Identifiler [18,19]. Only the first enrolled subject from a pair of first degree relatives was included in subsequent analyses.…”

Section: Statistical Analsysismentioning

confidence: 99%

Mutations and polymorphisms in hemoglobin genes and the risk of pulmonary hypertension and death in sickle cell disease

et al. 2007

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Pulmonary hypertension is a common complication of sickle cell disease (SCD) and a risk factor for early death. Hemolysis may participate in its pathogenesis by limiting nitric oxide (NO) bioavailability and producing vasculopathy. We hypothesized that hemoglobin mutations that diminish hemolysis in SCD would influence pulmonary hypertension susceptibility. Surprisingly, coincident a-thalassemia (Odds Ratio [OR] 5 0.95, 95% CI 5 0.46-1.94, P 5 NS) was not associated with pulmonary hypertension susceptibility in homozygous SCD. However, pulmonary hypertension cases were less likely to have hemoglobin SC (OR 5 0.18, 95% confidence interval [CI] 5 0.06-0.51, P 5 0.0005) or Sb 1 thalassemia (OR 5 0.25, 95% CI 5 0.06-1.16, P 5 0.10). These compound heterozygotes may be protected from pulmonary hypertension because of reduced levels of intravascular hemolysis, but develop this complication at a lower rate possibly due to the presence of non-hemolytic risk factors such as renal dysfunction, iron overload and advancing age. Despite this protective association, patients with SC who did develop pulmonary hypertension remained at significant risk for death during 49 months of followup (Hazard Ratio 5 8.20, P 5 0.0057). Am.

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Section: Statistical Analsysismentioning

confidence: 99%

Mutations and polymorphisms in hemoglobin genes and the risk of pulmonary hypertension and death in sickle cell disease

et al. 2007

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“…4 Genotypes of contaminated samples are assigned by the following process: if the genotypes of two samples at an SNP are the same, the genotypes of the two samples are not changed. If the genotypes are different, the genotypes of the two samples are assigned stochastically either as heterozygous or unchanged (the probability of the heterozygous and unchanged status is the same, 0.5 for each) for both samples.…”

Section: Simulation Studymentioning

confidence: 99%

“…3 For general detection of related samples, a likelihood ratio test based on posterior probability of genotype under certain relationships was proposed. 4 In the case of a family-based study, an identity-by-state (IBS)-based method 5,6 for a detection of errors in a sib-pair relationship was proposed, with the method using the summation of the IBS for a pair of sibs. Conversely, an identity-by-descent (IBD)-based method (PLINK 7 ) was proposed.…”

Section: Introductionmentioning

confidence: 99%

Detection of inappropriate samples in association studies by an IBS-based method considering linkage disequilibrium between genetic markers

Andoh

Sato²,

Sanada³

et al. 2010

J Hum Genet

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An association study is a popular study design to identify susceptibility genes for common complex diseases. In such a study, the presence of inappropriate samples, such as those derived from close relatives or showing DNA contamination, causes an inflation of type I error or a decrease of power. Here we propose an identity-by-state (IBS)-based detection method of inappropriate samples taking linkage disequilibrium (LD) into consideration. The test statistics is the mean of the proportion of alleles that are shared identical by state at each single nucleotide polymorphism (SNP) between each sample pair in an association study. A covariance of the number of shared alleles between two SNPs is introduced to consider LD. We show that type I error and power are estimated accurately in computer-simulated data, and that if the number of SNPs analyzed is small, the performance of detection of inappropriate samples is superior to the previous method in simulated LD. An application to real association study data showed that accuracy in estimating the distribution of test statistics improved if LD was considered. Sample pairs considered to be siblings were detected. These results suggested that an LD-considered IBS-based detection method is useful in identifying inappropriate samples in an association study.

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“…However, the STR data were not considered in further kinship analysis due to the fact that Wenk and colleagues' (1996) KI calculations using the HUMTH01 data yielded inconclusive results for the cluster burials with KI ranging between 1.0 to 4.2. Single polymorphic loci have been shown to provide little power to resolve biological relationships (Lins et al, 1996, Tzeng et al, 2000, Wenk et al, 1996.…”

Section: Adna Str Analysismentioning

confidence: 99%

“…This paper is a preliminary investigation of the efficacy of aDNA analyses to determine a kinship system from the archaeological record. Statistical approaches were borrowed from conventional kinship theory (as summarized in Wenk et al, 1996), and from forensic science (Allen et al, 1998) and used in the context of an archaeological burial site. Recovered aDNA from bone and tooth samples was submitted to mtDNA and STR amplification analyses to produce genotypes used in the calculation of the Probability of Matrilineal Kinship By Chance (PrMKBC), and a Kinship Index (KI).…”

mentioning

confidence: 99%

Determination of a kinship system using ancient DNA, mortuary practice, and historic records in an upper Canadian pioneer cemetery

Dudar¹,

Waye²,

Saunders³

2003

Intl J of Osteoarchaeology

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Recovered and amplified ancient DNA (aDNA), from a historically documented 19th century Upper Canadian pioneer cemetery produced genotypes that were used to infer a past societal kinship system. While the results from multiplex short tandem repeat (STR) amplifications showed an unreliable polymerase chain reaction (PCR) product, a single locus HUMTH01 analysis yielded reproducible data and an allelic frequency pattern not statistically different from modern populations. Mitochondrial (mt) DNA HVR II data showed that a combined cemetery database exhibited reduced haplotype diversity indicators, as well as clusters of probable maternally related burials. The chronological persistence and replacement of mtDNA clusters approximately every two generations suggests a patrilineal/patrilocal kinship structure from a virilocal burial program for the Harmony Road cemetery. Through the integration of the aDNA analysis with archaeological material culture, historic records, and other ethnohistoric sources of information, this conclusion is supported. In this study persisting patrilineally inherited surnames act as a surrogate for aDNA Y-chromosome haplotype analysis. These results suggest that aDNA applications on aggregate skeletal collections where sparse, or no ethnological or historical documentation exists, may result in incorrect population history inferences if the presence of a kinship interment bias is not considered.

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Determination of sibship in any two persons

Cited by 64 publications

References 3 publications

Mutations and polymorphisms in hemoglobin genes and the risk of pulmonary hypertension and death in sickle cell disease

Mutations and polymorphisms in hemoglobin genes and the risk of pulmonary hypertension and death in sickle cell disease

Detection of inappropriate samples in association studies by an IBS-based method considering linkage disequilibrium between genetic markers

Determination of a kinship system using ancient DNA, mortuary practice, and historic records in an upper Canadian pioneer cemetery

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