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Response to: DNA identification by pedigree likelihood ratio accommodating population substructure and mutations- authors' reply
Ranajit Chakraborty, Jianye Ge, Bruce Budowle
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-8
Abstract: In their letter to the editor, Egeland et al. [1] criticize the mutation model used in our paper [2], and propose that our comments about the mutation model used by Dawid et al. [3] are not convincing, because we do not provide any data in support of our assertions. Their criticisms are primarily based on three premises: 1) that our mutation model, presented on page 5 of our paper [2], is mathematically incorrect, because our equation 8 does not define a proper probability distribution (that is, the probabilities do not add to 1); 2) that our mutation model allows for production of alleles of zero or negative repeat sizes, which are not meaningful; and 3) that the model used in the paper by Dawid et al [3] uses the relationship between mutational transition probabilities and allele frequency on the basis that allele frequencies are representative of the stationary distribution of a mutation process, and hence, in the absence of natural selection, is presumably applicable to the sequence tagged repeat (STR) loci used in DNA forensics. Each of these issues needs further discussion, and we thank the authors for giving us an opportunity to explain them further.First, the mutation model, explained by equation 8 of page 5 of our paper [2], clearly states that the geometric distribution for Pr (X = x) applies to 'alleles to change by adding or subtracting an absolute number of x repeat units'. Hence, by definition x > 0, and as noted just after equation 8 'equal probabilities for gaining or losing repeats are assumed', it is incorrect to multiply the geometric terms by a factor of 2, as Egeland et al. have done [1]. Following this logic, our equation 8 mathematically represents a valid probability distribution, because the total probability of mutation (that is, X ≠ 0) becomes μ, by summing the individual terms over all non-zero positive integer values of X. In addition, we are not the first to use such formulations of a mutation model. Estoup et al. [4] used exactly the s
DNA identification by pedigree likelihood ratio accommodating population substructure and mutations
Jianye Ge, Bruce Budowle, Ranajit Chakraborty
Investigative Genetics , 2010, DOI: 10.1186/2041-2223-1-8
Abstract: Over the past two decades, forensic DNA typing has become widely accepted as a powerful tool in criminal and civil investigations. This technology has become invaluable in many missing-person identifications. There are a number of scenarios in which person identification is required: these include cases of war victims found in mass graves, missing soldiers or military personnel from past wars, people missing due to dynamic social reasons (for example, murder), remains from mass disasters due to natural catastrophes or terrorism attacks (for example, airplane crashes, the World Trade Center tragedy and the southeast Asia tsunami) and basic paternity testing. In attempts to identify these individuals, DNA profiles from unidentified people may be compared with direct reference samples of the missing person (antemortem samples), such as buccal swabs collected before their disappearance, or items they have used, such as toothbrushes, hairbrushes or preserved dental casts. In some cases, direct comparisons are not possible because an antemortem sample is not available, or the chain of custody may not be established reliably, reducing the confidence in an association. Alternatively, a missing person may be identified by kinship analysis using family reference samples (biological relatives such as parents, offspring, siblings or cousins) of the person to be identified.Traditionally, statistical inference was based on pairwise comparison of the DNA profiles of the unknown sample and a single family reference sample, and then ranking the likelihood ratios (LRs) for specified biological relationships. Numerous statistical methods are available for evaluation of kinship between individuals. Li and Sacks [1] first provided a general method to obtain the conditional probability for any pair of relatives. Jacquard [2] described the most general method for a pairwise relationship using nine condensed identity states. Thompson [3] pioneered the maximum likelihood method by summarizi
Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium : Evidence for gene duplications and extensive gene clustering
Harshavardhan Doddapaneni, Ranajit Chakraborty, Jagjit S Yadav
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-92
Abstract: Our analysis showed that P. chrysosporium P450ome could be classified into 12 families and 23 sub-families and is characterized by the presence of multigene families. A genome-level structural analysis revealed 16 organizationally homogeneous and heterogeneous clusters of tandem P450 genes. Analysis of our cloned cDNAs revealed structurally conserved characteristics (intron numbers and locations, and functional domains) among members of the two representative multigene P450 families CYP63 and CYP505 (P450foxy). Considering the unusually complex structural features of the P450 genes in this genome, including microexons (2–10 aa) and frequent small introns (45–55 bp), alternative splicing, as experimentally observed for CYP63, may be a more widespread event in the P450ome of this fungus. Clan-level phylogenetic comparison revealed that P. chrysosporium P450 families fall under 11 fungal clans and the majority of these multigene families appear to have evolved locally in this genome from their respective progenitor genes, as a result of extensive gene duplications and rearrangements.P. chrysosporium P450ome, the largest known todate among fungi, is characterized by tandem gene clusters and multigene families. This enormous P450 gene diversity has evolved by extensive gene duplications and intragenomic recombinations of the progenitor genes presumably to meet the exceptionally high metabolic demand of this biodegradative group of basidiomycetous fungi in ecological niches. In this context, alternative splicing appears to further contribute to the evolution of functional diversity of the P450ome in this fungus. The evolved P450 diversity is consistent with the known vast biotransformation potential of P. chrysosporium. The presented analysis will help design future P450 functional studies to understand the underlying mechanisms of secondary metabolism and oxidative biotransformation pathways in this model white rot fungus.The cytochrome P450 monooxygenases ("P450s") cons
Response to: Use of prior odds for missing persons identifications - authors' reply
Bruce Budowle, Jianye Ge, Ranajit Chakraborty, Harrell Gill-King
Investigative Genetics , 2012, DOI: 10.1186/2041-2223-3-3
Abstract: We are concerned that statisticians, such as Biedermann et al. [1], advocate the position that data may not be needed to support assumptions 'as long as probability is properly considered as an expression of personal belief'. At a time when the National Academy of Sciences [2] has urged the need for the forensic science community to provide reliable results based on 'objective' data, these authors' position cannot be reconciled. The Report noted (on its page 8), 'The simple reality is that the interpretation of forensic evidence is not always based on scientific studies to determine its validity ... A body of research is required to establish the limits and measures of performance and to address the impact of sources of variability and potential bias. Such research is sorely needed, but it seems to be lacking in most of the forensic disciplines that rely on subjective assessments of matching characteristics. These disciplines need to develop rigorous protocols to guide these subjective interpretations and pursue equally rigorous research and evaluation programs'. It is this approach that distinguishes science from other epistemologies. Then the Report called for research in its Recommendation 3 (page 23), 'Research is needed to address issues of accuracy, reliability, and validity in the forensic science disciplines ... [and in section c of Recommendation 3] the development of quantifiable measures of uncertainty in the conclusions of forensic analyses'.Foremost, none should abide the inclusion of overstated evidence in reports or legal proceedings as it can impinge on the presumption of innocence. The tenet of this presumption should be held dearly by all, and we as scientists should strive to reduce practices that cannot be supported. Biedermann et al. [1] appear to argue that, because there is 'subjectivity in science', one does not necessarily have to be held to a standard of justifying assumptions. It is well accepted that there is subjectivity in science. Inde
Use of prior odds for missing persons identifications
Bruce Budowle, Jianye Ge, Ranajit Chakraborty, Harrell Gill-King
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-15
Abstract: Mass disasters can result from natural, accidental and intentional causes. One of the tragedies of such events is loss of lives. Many jurisdictions seek to identify the victims so they can be returned to their respective families, for investigative purposes and/or for legal reasons (for example, resolution of estates, probate and criminal investigations). As in other forensic applications, identification is a matter of evaluating variables to reduce the pool of candidates with the intent of approaching individualization. Various characteristics or traits are used to assist in the identification of the human remains, including but not limited to skeletal features (for example, sex, age, stature and ancestry), dental comparisons, fingerprints, distinguishing marks (for example, tattoos and scars), medical devices and implants, other unique features, DNA profiles and, to a much lesser extent, eyewitness accounts and sometimes personal items. However, the frequency of the observed value of each variable needs to be assessed appropriately to effectively reduce the candidate pool.For the past two decades, DNA typing has played a more prominent role in the identification of human remains, and particularly so for highly decomposed and fragmented remains [1-12]. DNA profiles from recovered unidentified human remains may be compared with direct reference samples (for example, toothbrush, razor and hairbrush) and/or profiles from relatives (that is, an indirect comparison or kinship analysis) to identify possible associations. The strength of the genetic associations is often quantified by calculating a likelihood ratio (LR). The LR is used to evaluate whether there is evidence to support a specified biological relationship or direct identification. The literature is replete with approaches to calculating the LRs for direct and kinship analyses [5,13-23] and therefore need not be discussed further herein.The genetic evidence (that is, LR) can be combined with nongenetic eviden
Distribution and Effects of Nonsense Polymorphisms in Human Genes
Yumi Yamaguchi-Kabata, Makoto K. Shimada, Yosuke Hayakawa, Shinsei Minoshima, Ranajit Chakraborty, Takashi Gojobori, Tadashi Imanishi
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003393
Abstract: Background A great amount of data has been accumulated on genetic variations in the human genome, but we still do not know much about how the genetic variations affect gene function. In particular, little is known about the distribution of nonsense polymorphisms in human genes despite their drastic effects on gene products. Methodology/Principal Findings To detect polymorphisms affecting gene function, we analyzed all publicly available polymorphisms in a database for single nucleotide polymorphisms (dbSNP build 125) located in the exons of 36,712 known and predicted protein-coding genes that were defined in an annotation project of all human genes and transcripts (H-InvDB ver3.8). We found a total of 252,555 single nucleotide polymorphisms (SNPs) and 8,479 insertion and deletions in the representative transcripts in these genes. The SNPs located in ORFs include 40,484 synonymous and 53,754 nonsynonymous SNPs, and 1,258 SNPs that were predicted to be nonsense SNPs or read-through SNPs. We estimated the density of nonsense SNPs to be 0.85×10?3 per site, which is lower than that of nonsynonymous SNPs (2.1×10?3 per site). On average, nonsense SNPs were located 250 codons upstream of the original termination codon, with the substitution occurring most frequently at the first codon position. Of the nonsense SNPs, 581 were predicted to cause nonsense-mediated decay (NMD) of transcripts that would prevent translation. We found that nonsense SNPs causing NMD were more common in genes involving kinase activity and transport. The remaining 602 nonsense SNPs are predicted to produce truncated polypeptides, with an average truncation of 75 amino acids. In addition, 110 read-through SNPs at termination codons were detected. Conclusion/Significance Our comprehensive exploration of nonsense polymorphisms showed that nonsense SNPs exist at a lower density than nonsynonymous SNPs, suggesting that nonsense mutations have more severe effects than amino acid changes. The correspondence of nonsense SNPs to known pathological variants suggests that phenotypic effects of nonsense SNPs have been reported for only a small fraction of nonsense SNPs, and that nonsense SNPs causing NMD are more likely to be involved in phenotypic variations. These nonsense SNPs may include pathological variants that have not yet been reported. These data are available from Transcript View of H-InvDB and VarySysDB (http://h-invitational.jp/varygene/).
p53 Codon 72 Polymorphism and Risk of Cervical Cancer
Biological Research , 2003, DOI: 10.4067/S0716-97602003000200017
Abstract: storey et al. (1998) implicated the proline/argine polymorphism of the codon 72 of the tumor-suppressor gene p53 in the development of cervical cancer (cc) with the observation that the p53 protein is more efficiently inactivated by the e6 oncoprotein of human papillomavirus in p53 arginine as compared with its proline isoform. these authors further noted that in the united kingdom, individuals homozygous for the arginine allele were several times more susceptible to hpv-associated tumorigenesis that proline/arginine heterozygotes. subsequent studies in different countries failed to unanimously confirm this association. motivated by the high incidence of cc in chile, we undertook a case control study obtaining the following frequencies for genotypes pp, ap and aa in 60 icc cases and 53 carefully selected controls: 0.067, 0.250, 0.683 and 0.075, 0.453, 0.472 respectively. a significant difference (x2 = 3.19 p < 0.02) and an odds ratio of 2.62 supported storey et al (1998)'s results. in addition, rejecting previous hypotheses about the world distribution of the p53 codon 72 polymorphism, we conclude that this distribution most likely represents ancient human dispersal routes. several methodological and biological explanations for the results obtained in previous negative association studies are briefly discussed.
Common SNPs in FTO Gene Are Associated with Obesity Related Anthropometric Traits in an Island Population from the Eastern Adriatic Coast of Croatia
Ge Zhang,Rebekah Karns,Nina Smolej Narancic,Guangyun Sun,Hong Cheng,Sasa Missoni,Zijad Durakovic,Pavao Rudan,Ranajit Chakraborty,Ranjan Deka
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010375
Abstract: Multiple studies have provided compelling evidence that the FTO gene variants are associated with obesity measures. The objective of the study was to investigate whether FTO variants are associated with a broad range of obesity related anthropometric traits in an island population.
Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes
Ritesh Kaushal, Daniel Woo, Prodipto Pal, Mary Haverbusch, Huifeng Xi, Charles Moomaw, Padmini Sekar, Brett Kissela, Dawn Kleindorfer, Matthew Flaherty, Laura Sauerbeck, Ranajit Chakraborty, Joseph Broderick, Ranjan Deka
BMC Medical Genetics , 2007, DOI: 10.1186/1471-2350-8-49
Abstract: At the APOE locus, no individual SNP was associated with SAH after correction for multiple comparisons. Haplotype analysis revealed significant association of the major haplotype (Hap1) in APOE with SAH (p = 0.001). The association stemmed from both the 5' promoter and the 3' region of the APOE gene. APOE ε2 and ε 4 were not significantly associated with SAH. No association was observed for ELN at genotype, allele, or haplotype level and our study failed to confirm previous reports of ELN association with aneurysmal SAH.This study suggests a role of the APOE gene in the etiology of aneurysmal SAH.Non-traumatic, spontaneous subarachnoid hemorrhage (SAH) affects 16,000 to 17,000 individuals each year in the United States [1-3]. SAH has a 30-day mortality rate exceeding 40%, and surviving patients often demonstrate significant morbidity [2,4]. Over 80% of SAH can be attributed to intracranial aneurysm (IA) rupture. Familial aggregation studies of SAH have consistently identified an increased risk of a first-degree relative with SAH or family history of SAH independent of smoking and hypertension [5].Variants of the apolipoprotein E (APOE) gene have been associated with Alzheimer's disease, lipid disorders and cardiovascular disease [6-8]. Previous studies have demonstrated that APOE ε4 and/or APOE ε2 are associated with lobar intracerebral hemorrhage (ICH) [9,10]. We recently reported that haplotypes which include polymorphisms in the 5' untranslated region of the APOE gene are risk factors for lobar ICH [11]. Specific to SAH, Kokubo et al. [12] found significant association of APOE ε4 with SAH in a Japanese population. Niskakangas et al. [13] reported association of APOE ε4 with adverse outcome after aneurysmal SAH. No study on other polymorphisms of APOE with regard to risk of SAH has yet been reported.In addition to APOE, the elastin (ELN) gene emerged as a putative gene for IA after linkage was found on 7q11, where ELN is located [14]. However, prior association st
Finding Missing Heritability in Less Significant Loci and Allelic Heterogeneity: Genetic Variation in Human Height
Ge Zhang, Rebekah Karns, Guangyun Sun, Subba Rao Indugula, Hong Cheng, Dubravka Havas-Augustin, Natalija Novokmet, Zijad Durakovic, Sasa Missoni, Ranajit Chakraborty, Pavao Rudan, Ranjan Deka
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0051211
Abstract: Genome-wide association studies (GWAS) have identified many common variants associated with complex traits in human populations. Thus far, most reported variants have relatively small effects and explain only a small proportion of phenotypic variance, leading to the issues of ‘missing’ heritability and its explanation. Using height as an example, we examined two possible sources of missing heritability: first, variants with smaller effects whose associations with height failed to reach genome-wide significance and second, allelic heterogeneity due to the effects of multiple variants at a single locus. Using a novel analytical approach we examined allelic heterogeneity of height-associated loci selected from SNPs of different significance levels based on the summary data of the GIANT (stage 1) studies. In a sample of 1,304 individuals collected from an island population of the Adriatic coast of Croatia, we assessed the extent of height variance explained by incorporating the effects of less significant height loci and multiple effective SNPs at the same loci. Our results indicate that approximately half of the 118 loci that achieved stringent genome-wide significance (p-value<5×10?8) showed evidence of allelic heterogeneity. Additionally, including less significant loci (i.e., p-value<5×10?4) and accounting for effects of allelic heterogeneity substantially improved the variance explained in height.
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