Pedigree Analysis Research Articles

Genetic ancestry in Puerto Rican afro-descendants illustrates diverse histories of African diasporic populations.

Genetic studies of contemporary Puerto Ricans reflect a demographic history characterized by admixture between Indigenous American, African, and European peoples. While previous studies provide genetic perspectives on the general Puerto Rican population, less is known about the island's sub-populations, specifically Afro-Puerto Ricans. In this study, the genetic ancestry of Afro-Puerto Ricans is characterized and compared to other Caribbean populations. Thirty DNA samples collected among self-identified Puerto Ricans of African descent in Loíza (n = 2), Piñones (n = 13), San Juan (n = 2), Mayagüez (n = 9), and Ponce (n = 4), were genotyped at 750,000 loci on the National Geographic Genochip. We then applied unsupervised clustering and dimensionality-reduction methods to detect continental and subcontinental African and European genetic ancestry patterns. Admixture analyses reveal that on average, the largest genetic ancestry component for Afro-Puerto Ricans is African in origin, followed by European and Indigenous American genetic ancestry components. African biogeographic origins of Afro-Puerto Ricans align most closely with contemporary peoples of Lower Guinea and the Bight of Biafra, while the European genetic ancestry component is most similar to contemporary Iberian, Italian, and Basque populations. These findings contrast with the biogeographic origins of comparative Barbadian and Puerto Rican populations. Our results suggest that while there are similarities with regard to general patterns of genetic ancestry among African descendants in the Caribbean, there is previously unrecognized regional heterogeneity, including among Puerto Rican sub-populations. These results are also consistent with available historical sources, while providing depth absent from the documentary record, particularly with regard to African ancestry.

Spinocerebellar ataxia type 10 and Huntington disease-like 2 in Venezuela: Further evidence of two different ancestral founder effects.

The American continent populations have a wide genetic diversity, as a product of the admixture of three ethnic groups: Amerindian, European, and African Sub-Saharan. Spinocerebellar ataxia type 10 (SCA10) and Huntington disease-like 2 (HDL2) have very ancient ancestral origins but are restricted to two populations: Amerindian and African Sub-Saharan, respectively. This study aimed to investigate the genetic epidemiological features of these diseases in Venezuela. In-phase haplotypes with the expanded alleles were established in seven unrelated index cases diagnosed with SCA10 and in 11 unrelated index cases diagnosed with HDL2. The origins of remote ancestors were recorded. The geographic origin of the ancestors showed grouping in clusters. SCA10 had a minimal general prevalence of 1:256,174 families in the country, but within the identified geographic clusters, the prevalence ranged from 5 per 100,000 to 43 per 100,000 families. HDL2 had a general prevalence of 1:163,016 families, however, within the clusters, the prevalence ranged from 31 per 100,000 to 60 per 100,000 families. The locus-specific haplotype shared by all families worldwide, including the Venezuelans, supports a single old ancestral origin in each case. Knowing the genetic ancestry and geographic origins of patients in Ibero-American mixed populations could have significant diagnostic implications; thus, both diseases in Venezuela should always be first explored in patients with a suggestive phenotype and ancestors coming from the same known geographic clusters.

Coronary artery disease polygenic risk score in patients undergoing coronary angiography and risk of future revascularization

Abstract Background Coronary artery disease (CAD) polygenic risk score (PRS) is a strong predictor of incident CAD. The role of CAD PRS in patients with known or suspected CAD already presenting for invasive coronary angiography remains poorly understood. Purpose We aimed to (i) study the association between CAD PRS and coronary angiography traits, and (ii) determine whether CAD PRS can predict risk of future revascularization after an initial coronary angiogram. Methods Patients who underwent coronary angiography at a single hospital and were part of its biobank were included in the study. Participants were classified into 3 risk groups based on CAD PRS distribution–low (0-20%), intermediate (21-80%), and high (81-100%)–computed from a recently reported PRS comprised of 1,296,172 variants (GPSMult, PGS003725). Revascularization was defined as a composite of coronary artery bypass graft and percutaneous coronary intervention with a 3-month blocking window after the initial angiogram. Associations between coronary stenosis severity and burden, and CAD PRS were assessed using multinomial logistic regression adjusted for age, sex, and genetic ancestry. The cumulative incidence of revascularization was tested using Fine-Gray regression accounting for competing risk of all-cause mortality and compared across CAD PRS strata by log-rank test. Results Among 3,518 participants (29.90% female, mean age 63.29±12.14 years), 2,568 (73%) had angiographic evidence of CAD – 340 (13.24%) mild, 346 (13.47%) moderate, and 1,882 (73.29%) severe. Out of those with CAD, 844 (32.87%) presented with acute coronary syndromes (ACS) and 1,724 (67.13%) with stable CAD. CAD PRS was strongly associated with angiographic presence of CAD (OR 2.62, 95%CI 2.08-3.29) and this did not differ among patients presenting with ACS vs. stable CAD (Fig1A). The association was weakest for mild CAD (OR 1.14, 95%CI 0.77-1.68) and strongest for severe CAD (OR 3.04, 95%CI 2.40-3.84). Besides severity, CAD PRS was also strongly associated with angiographic burden of CAD with the strongest association observed for presence of left main coronary stenosis (OR 2.63, 95%CI 1.86-3.73). Each standard deviation increase in CAD PRS was associated with a 10-point increase in the Gensini score, a continuous measure of angiographic burden of CAD (p<2e-16) (Fig1B). Over a mean follow-up period of 9.26±5.81 years, 659 (18.73%) patients required revascularization at a mean period of 5.31±4.69 years. Risk of revascularization varied dramatically by CAD PRS; HR was 1.64 (95%CI 1.28-2.10, p=8.7e-5) for high vs. low CAD PRS (Fig2). CAD PRS remained predictive of future revascularization even after adjusting for the angiographic burden of CAD at baseline (HR 1.41, 95%CI 1.09-1.82, p=7.9e-3). Conclusion CAD PRS is strongly associated with severity and burden of CAD assessed on coronary angiography and is predictive of future risk of revascularization even after accounting for baseline disease burden.Figure 1.CAD PRS and angiographic traitsFigure 2.CAD PRS and revascularization

Obesity-dependent selection of driver mutations in cancer.

Obesity is a risk factor for cancer, but whether obesity is linked to specific genomic subtypes of cancer is unknown. We examined the relationship between obesity and tumor genotype in two clinicogenomic corpora. Obesity was associated with specific driver mutations in lung adenocarcinoma, endometrial carcinoma and cancers of unknown primaries, independent of clinical covariates, demographic factors and genetic ancestry. Obesity is therefore a driver of etiological heterogeneity in some cancers.

Genetic Diversity and Forensic Utility of X-STR Loci in Punjabi and Kashmiri Populations: Insights into Population Structure and Ancestry

Background: X-chromosomal short tandem repeats (X-STRs) are crucial in forensic applications, particularly in complex kinship cases, and play an important role in population genetics. However, there is limited data on X-STR variation in Pakistani populations, especially among ethnic groups like Kashmiri and Punjabi. Methodology: This study investigates the forensic and genetic properties of 12 X-STRs from the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 125 families (75 Kashmiri, 50 Punjabi) from Azad Jammu and Kashmir and Punjab, Pakistan. Results: In both populations, a total of 222 alleles were identified across the 12 X-STR loci (Punjabi 171 alleles, Kashmiri 161 alleles), with allele frequencies ranging from 0.0056 to 0.3033. DXS10148 was the most polymorphic locus with 28 alleles, while DXS7132 was the least polymorphic with 9 alleles. Most loci were in linkage equilibrium, except for the DXS10135/DXS10148 pair in males, with no loci exhibiting significant linkage disequilibrium in females. The combined power of discrimination was 0.999 999 9977 for Kashmiri males, 0.999 999 999 999 9746 for Kashmiri females, and 0.999 999 999 999 9781 for Punjabi females. In Kashmiri males, 34, 31, 28, and 32 haplotypes were observed across the four linkage groups (LG1, LG2, LG3, and LG4), though these groups did not form stable haplotypes, as indicated by Linkage Equilibrium within and significant Linkage Disequilibrium between groups. Conclusions: Genetic structure analysis using Principal Component Analysis and STRUCTURE revealed distinct clustering patterns for the Kashmiri and Punjabi populations, indicating unique genetic backgrounds and ancestry influences, particularly distinguishing them from East Asian populations. This study provides a comprehensive analysis of X-STR variation in Punjabi and Kashmiri populations, offering valuable insights for forensic and population genetic studies.

Y chromosome sequencing data suggest dual paths of haplogroup N1a1 into Finland.

The paternally inherited Y chromosome is highly informative of genetic ancestry, therefore making it useful in studies of population history. In Finland, two Y-chromosomal haplogroups reveal the major substructure of the population: N1a1 enriched in the northeast and I1a in the southwest, suggested to reflect eastern and western ancestry contributions to the population. Yet, beyond these major Y-chromosomal lineages, the distribution of finer-scale Y-chromosomal variation has not been assessed in Finland. Here, we provide the most comprehensive Y-chromosomal study among the Finns to date, exploiting sequences for 1802 geographically mapped Finnish Y chromosomes from the FINRISK project. We assessed the distribution of common Y-chromosomal haplogroups (frequency ≥1%) throughout 19 Finnish regions and compared the autosomal genetic backgrounds of the Y-chromosomal haplogroups. With such high-resolution data, we were able to find previously unreported sublineages and resolve phylogenetic relationships within haplogroups N1a1 (64%), I1a (25%), R1a (4.3%), and R1b (4.8%). We further find novel geographical enrichment patterns among these Y-chromosomal haplogroups, most notably observed for haplogroup N1a1 dividing into two lineages with differing distributions. While sublineage N-Z1934 (42%) followed a northeastern enrichment pattern observed for all N1a1 carriers in general, sublineage N-VL29 (22%) displayed an enrichment in the southwest. Further, the carriers of N-VL29 showed a higher proportion of southwestern autosomal ancestry compared to carriers of N-Z1934. Collectively, these results point to distinct demographics within haplogroup N1a1, possibly induced by two distinct arrival routes into Finland. Overall, our study suggests a more complex genetic population history for Finns than previously proposed.

Molecular and Clinical Characterization of a Cohort of Autosomal Recessive Sensorineural Hearing Loss in Egyptian Patients

Hearing loss (HL) is one of the most common health problems worldwide. Autosomal recessive non-syndromic sensorineural hearing loss (ARNSHL) represents a large portion of congenital hereditary HL. Our study was conducted on 13 patients from 13 unrelated families. The majority of patients presented with congenital severe to profound bilateral sensorineural HL. All patients were subjected to detailed family history and three-generation pedigree analysis to exclude any environmental cause and to ensure an autosomal recessive mode of inheritance. Molecular analysis was performed using the whole exome sequencing (WES) technique for the recruited patients. Three variants in the MYO7A and OTOF genes were reported for the first time in patients with ARNSHL (one nonsense, one frameshift, and one splice variant). Ten previously reported variants were detected in seven genes (GJB2, MYO15A, BSND, OTOF, CDH23, SLC26A4, and TMIE). They varied between missense, nonsense, frameshift, and splice variants. This study expands the molecular spectrum of two types of autosomal recessive deafness (types 2 and 9).

SNP Genotype Imputation in Forensics—A Performance Study

Background/Objectives: Emerging forensic genetic applications, such as forensic investigative genetic genealogy (FIGG), advanced DNA phenotyping, and distant kinship inference, increasingly require dense SNP genotype datasets. However, forensic-grade DNA often contains missing genotypes due to its quality and quantity limitations, potentially hindering these applications. Genotype imputation, a method that predicts missing genotypes, is widely used in population and medical genetics, but its utility in forensic genetics has not been thoroughly explored. This study aims to assess the performance of genotype imputation in forensic contexts and determine the conditions under which it can be effectively applied. Methods: We employed a simulation-based approach to generate realistic forensic SNP genotype datasets with varying numbers, densities, and qualities of observed genotypes. Genotype imputation was performed using Beagle software, and the performance was evaluated based on the call rate and imputation accuracy across different datasets and imputation settings. Results: The results demonstrate that genotype imputation can significantly increase the number of SNP genotypes. However, imputation accuracy was dependent on factors such as the quality of the original genotype data and the characteristics of the reference population. Higher SNP density and fewer genotype errors generally resulted in improved imputation accuracy. Conclusions: This study highlights the potential of genotype imputation to enhance forensic SNP datasets but underscores the importance of optimizing imputation parameters and understanding the limitations of the original data. These findings will inform the future application of imputation in forensic genetics, supporting its integration into forensic workflows.

Investigation of the association of the MLPH gene with seasonal canine flank alopecia in Rhodesian Ridgeback dogs

BackgroundCanine flank alopecia (CFA) is a skin condition in dogs characterized by non-inflammatory, seasonally recurring episodes of localized hair loss and often hyperpigmentation of the affected skin. A genetic basis is suspected because of the predisposition in certain breeds, such as the Rhodesian Ridgeback (RR). This study investigated the possible role of the canine melanophylin (MLPH) gene in CFA among RRs through pedigree analysis and MLPH genotyping.ResultsWe included 24 CFA-affected and 12 non-CFA-affected control RRs. Pedigree analysis revealed inbreeding loops and close family relationships among the CFA-affected dogs, indicating the potential heritability of CFA. MLPH genotyping revealed 3/24 (12.5%) affected dogs and 1/12 (8.3%) control dogs to be heterozygous (Dd) for the dilute (d) allele, indicating no difference between these groups. None of the dogs were found to be homozygous (dd). Statistical analysis did not reveal an association between the MLPH-d allele and CFA.ConclusionsThe familial patterns among affected RRs observed through pedigree analysis suggest a potential genetic component in CFA. However, our findings from the MLPH genotyping did not reveal that the MLPH gene is involved in this skin condition in RRs. However, further genetic studies are needed to clarify the etiology of CFA in RR dogs.

PALB2 analysis in the diagnostic process of breast cancer: An Italian monocentric experience.

The clinical utility of germline BRCA1 and BRCA2 testing is well established in patients with family history suggestive for hereditary breast and ovarian cancer syndrome. Recently, germline PALB2 pathogenic variants were also associated with an increased risk of breast and other cancers and, in the Italian population, it has been described in few studies without a systematic germline analysis of BRCA1, BRCA2 and PALB2. In this study, we described ASST Sette Laghi cancer genetic counselling services' experience in the analysis of 402 patients with suspected breast and ovarian cancer syndrome, by using BRCA1, BRCA2 and PALB2 germline genetic test. The frequency of PALB2 pathogenic variants was 1.2% compared to 3.5% and 3.2% for BRCA1 and BRCA2, respectively, whereas class 3 variants were detected in 0.3% and 0.5% of the BRCA1 and BRCA2 investigated patients, respectively. PALB2 pathogenic variants were identified in patients with a strong family history for breast cancer. Moreover, PALB2 variants were significantly associated with a younger age of breast cancer onset (mean age, 40.25 years) compared to wild-type patients (mean age 51.2 years, p-value = 0.0331). Similar to BRCA-associated breast cancer, the majority of PALB2 breast cancers were identified at an advanced clinical stage. Pedigree analysis revealed a family history of breast and ovarian cancer syndrome in all PALB2 pathogenic variants carriers (early breast cancer onset, bilateral breast cancer and ovarian cancer). In conclusion, the germline analysis of BRCA1, BRCA2 and PALB2 should be included in breast cancer clinical practice as a not negligible number of PALB2 carriers could be identified and referred to specific surveillance protocols.

Inferring ancestry with the hierarchical soft clustering approach tangleGen.

Understanding the genetic ancestry of populations is central to numerous scientific and societal fields. It contributes to a better understanding of human evolutionary history, advances personalized medicine, aids in forensic identification, and allows individuals to connect to their genealogical roots. Existing methods, such as ADMIXTURE, have significantly improved our ability to infer ancestries. However, these methods typically work with a fixed number of independent ancestral populations. As a result, they provide insight into genetic admixture, but do not include a hierarchical interpretation. In particular, the intricate ancestral population structures remain difficult to unravel. Alternative methods with a consistent inheritance structure, such as hierarchical clustering, may offer benefits in terms of interpreting the inferred ancestries. Here, we present tangleGen, a soft clustering tool that transfers the hierarchical machine learning framework Tangles, which leverages graph theoretical concepts, to the field of population genetics. The hierarchical perspective of tangleGen on the composition and structure of populations improves the interpretability of the inferred ancestral relationships. Moreover, tangleGen adds a new layer of explainability, as it allows identifying the SNPs that are responsible for the clustering structure. We demonstrate the capabilities and benefits of tangleGen for the inference of ancestral relationships, using both simulated data and data from the 1000 Genomes Project.

Genetic structure and common ancestry expose the dingo-dog hybrid myth

Abstract The evolutionary history of canids has been shown to be complex, with hybridization and domestication confounding our understanding of speciation among various canid lineages. The dingo is a recent canid lineage that was completely isolated from other canids for over 5000 years on the Australian mainland, but the introduction of domestic dogs in 1788 has placed doubt on its independence, with recent studies highlighting hybridization between dingoes and domestic dogs. Using genomic single nucleotide polymorphism data from 434 Australian canid samples, we explicitly test for introgression between closely related canid groups and dingoes. We found no evidence of introgression between dingoes and domestic dogs and show that previous work has likely mischaracterized shared ancestral genetic variation as evidence for hybridization. Further, New Guinea Singing Dogs are the only canid group that significantly shared genetic variation with dingoes, which fits with our understanding of previous phylogenetic analyses. Despite more recent sympatric distributions with dogs, dingoes have likely maintained their independence since their arrival in Australia, even in areas with high lethal control, indicating that their evolutionary trajectory is currently being conserved. The future conservation of the dingo lineage will require policies that promote coexistence pathways between humans and dingoes that protect rangeland systems and the dingoes’ evolutionary future.

Genomic Exploration of Essential Hypertension in African-Brazilian Quilombo Populations: A Comprehensive Approach with Pedigree Analysis and Family-Based Association Studies.

Essential Hypertension (EH) is a global health issue. Despite extensive research, much of EH heritability remains unexplained. We investigated the genetic basis of EH in African-derived individuals from partially isolated quilombo populations in Vale do Ribeira (SP-Brazil). Samples from 431 individuals (167 affected, 261 unaffected, 3 unknown) were genotyped using a 650k SNP array. Estimated global ancestry proportions were 47% African, 36% European, and 16% Native American. We constructed six pedigrees using additional data from 673 individuals and created three non-overlapping SNP subpanels. We phased haplotypes and performed local ancestry analysis to account for admixture. Genome-wide linkage analysis (GWLA) and fine-mapping via family-based association studies (FBAS) were conducted, prioritizing EH-associated genes through systematic approach involving databases like PubMed, ClinVar, and GWAS Catalog. Linkage analysis identified 22 regions of interest (ROIs) with LOD scores ranging 1.45-3.03, encompassing 2363 genes. Fine-mapping (FBAS) identified 60 EH-related candidate genes and 117 suggestive/significant variants. Among these, 14 genes, including PHGDH , S100A10 , MFN2 , and RYR2 , were strongly related to hypertension harboring 29 suggestive/significant SNPs. Through a complementary approach - combining admixture-adjusted GWLA based on Markov chain Monte Carlo methods, FBAS on known and imputed data, and gene prioritizing - new loci, variants, and candidate genes were identified. These findings provide targets for future research, replication in other populations, facilitate personalized treatments, and improve public health towards African-derived underrepresented populations. Limitations include restricted SNP coverage, self-reported pedigree data, and lack of available EH genomic studies on admixed populations for independent validation, despite the performed genetic correlation analyses using summary statistics.

Methylation Clocks Do Not Predict Age or Alzheimer's Disease Risk Across Genetically Admixed Individuals.

Epigenetic clocks that quantify rates of aging from DNA methylation patterns across the genome have emerged as a potential biomarker for risk of age-related diseases, like Alzheimer's disease (AD), and environmental and social stressors. However, methylation clocks have not been validated in genetically diverse cohorts. Here we evaluate a set of methylation clocks in 621 AD patients and matched controls from African American, Hispanic, and white co-horts. The clocks are less accurate at predicting age in genetically admixed individuals, especially those with substantial African ancestry, than in the white cohort. The clocks also do not consistently identify age acceleration in admixed AD cases compared to controls. Methylation QTL (meQTL) commonly influence CpGs in clocks, and these meQTL have significantly higher frequencies in African genetic ancestries. Our results demonstrate that methylation clocks often fail to predict age and AD risk beyond their training populations and suggest avenues for improving their portability.

SPLENDID incorporates continuous genetic ancestry in biobank-scale data to improve polygenic risk prediction across diverse populations.

Polygenic risk scores are widely used in disease risk stratification, but their accuracy varies across diverse populations. Recent methods large-scale leverage multi-ancestry data to improve accuracy in under-represented populations but require labelling individuals by ancestry for prediction. This poses challenges for practical use, as clinical practices are typically not based on ancestry. We propose SPLENDID, a novel penalized regression framework for diverse biobank-scale data. Our method utilizes ancestry principal component interactions to model genetic ancestry as a continuum within a single prediction model for all ancestries, eliminating the need for discrete labels. In extensive simulations and analyses of 9 traits from the All of Us Research Program (N=224,364) and UK Biobank (N=340,140), SPLENDID significantly outperformed existing methods in prediction accuracy and model sparsity. By directly incorporating continuous genetic ancestry in model training, SPLENDID stands as a valuable tool for robust risk prediction across diverse populations and fairer clinical implementation.

AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software.

Admixture is a fundamental process that has shaped levels and patterns of genetic variation in human populations. RFMIX version 2 (RFMIX2) utilizes a robust modeling approach to identify the genetic ancestries in admixed populations. However, this software does not have a built-in method to visually summarize the results of analyses. Here, we introduce the AncestryGrapher toolkit, which converts the numerical output of RFMIX2 into graphical representations of global and local ancestry (i.e., the per-individual ancestry components and the genetic ancestry along chromosomes, respectively). To demonstrate the utility of our methods, we applied the AncestryGrapher toolkit to visualize the global and local ancestry of individuals in the North African Mozabite Berber population from the Human Genome Diversity Panel (HGDP). Our results showed that the Mozabite Berbers derived their ancestry from the Middle East, Europe, and sub-Saharan Africa (global ancestry). We also found that the population origin of ancestry varied considerably along chromosomes (local ancestry). For example, we observed variance in local ancestry in the genomic region on chromosome 2 containing the regulatory sequence in the MCM6 gene associated with lactase persistence (LP), a human adaptive trait tied to the cultural development of adult milk consumption. Overall, the AncestryGrapher toolkit facilitates the exploration, interpretation, and reporting of ancestry patterns in human populations. The AncestryGrapher toolkit is free and open source on https://github.com/alisi1989/RFmix2-Pipeline-to-plot. Supplementary data are available at Bioinformatics online.

Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago.

Mainland Japanese have been recognized as having dual ancestry, originating from indigenous Jomon people and immigrants from continental East Eurasia. Although migration from the continent to the Japanese Archipelago continued from the Yayoi to the Kofun period, our understanding of these immigrants, particularly their origins, remains insufficient due to the lack of high-quality genome samples from the Yayoi period, complicating predictions about the admixture process. To address this, we sequenced the whole nuclear genome of a Yayoi individual from the Doigahama site in Yamaguchi prefecture, Japan. A comprehensive population genetic analysis of the Doigahama Yayoi individual, along with ancient and modern populations in East Asia and Northeastern Eurasia, revealed that the Doigahama Yayoi individual, similar to Kofun individuals and modern Mainland Japanese, had three distinct genetic ancestries: Jomon-related, East Asian-related, and Northeastern Siberian-related. Among non-Japanese populations, the Korean population, possessing both East Asian-related and Northeastern Siberian-related ancestries, exhibited the highest degree of genetic similarity to the Doigahama Yayoi individual. The analysis of admixture modeling for Yayoi individuals, Kofun individuals, and modern Japanese respectively supported a two-way admixture model assuming Jomon-related and Korean-related ancestries. These results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula.

Genomic and Serological Rheumatoid Arthritis Biomarkers, MUC5B Promoter Variant, and Interstitial Lung Abnormalities.

Rheumatoid arthritis (RA) has been implicated in interstitial lung disease (ILD) as majority of studies have been comprised of patients with known RA. However, it remains unclear whether an underlying risk for RA in combination with genetic risk for pulmonary fibrosis is associated with radiological markers of early lung injury and fibrosis in broader population samples. Determine whether genetic and serological biomarkers of RA risk in combination with the MUC5B (rs35705950) risk allele (T) are associated with interstitial lung abnormalities (ILA) on computed tomography (CT) scans. Associations of RA-risk HLA-DRB1 alleles (*04:01, *04:08, *04:05, *04:04, *10:01) and serum RA autoantibodies with ILA in the Multi-Ethnic Study of Atherosclerosis (MESA, n=4,018) and COPDGene (n=5,963) cohorts were modeled using logistic regression and adjusted for age, sex, self-reported race and ethnicity, smoking history, body mass index, and principal components of genetic ancestry. The prevalence of an RA risk HLA-DRB1 allele was 16.5% and 21.9% in MESA and COPDGene, respectively. ILA was present in 3.9% and 11% in MESA and COPDGene, respectively. An RA risk HLA-DRB1 allele was not significantly associated with ILA in MESA and COPDGene. In MESA, higher serum levels of IgA rheumatoid factor (RF) and anti-cyclic citrullinated peptide were associated with an odds ratio (OR) for ILA of 1.20 (95% CI 1.07-1.35) and 1.19 (95% CI 1.04-1.37), respectively. Among smokers without baseline ILA, per doubling of IgM RF was associated with an OR for ILA 10 years later of 1.25 (95% CI 1.08-1.43). Associations were not significantly different by MUC5B risk allele status. RA-related HLA-DRB1 alleles were not associated with ILA, whereas higher serum levels of IgM RF among smokers without baseline ILA were associated with subsequent ILA.

Common roots of Riza Fakhretdin and the Service Tatars Baishevs in the context of Genetic Genealogy

The publication presents a comparative analysis of the results of genetic studies and information from the funds of the “Local Order” (f. 1209) and “Landrat Books and Census Records” (f. 350) of the Russian State Archive of Ancient Acts concerning the genealogy of the famous scientist-educator, historian, theologian and public figure Rizaetdin Fakhretdin. As a result of the study, the plausibility of the family legends of R. Fakhretdin about the origin of his ancestors from the Shirdan village of Sviyazhsk district, was proven, their common origin with the famous service Service Tatar family of the Baishevs was shown. For citation: Vladimirov O.O. Common roots of Riza Fakhretdin and the Service Tatars Baishevs in the context of Genetic Genealogy. From History and Culture of Peoples of the Middle Volga Region. 2024, vol.14, no.3, pp.146–153. https://doi.org/10.22378/2410-0765.2024-14-3.146-153 (In Russian)

Evaluation of Four Forensic Investigative Genetic Genealogy Analysis Approaches with Decreased Numbers of SNPs and Increased Genotyping Errors

Background: Forensic investigative genetic genealogy (FIGG) has developed rapidly in recent years and is considered a novel tool for crime investigation. However, crime scene samples are often of low quality and quantity and are challenging to analyze. Deciding which approach should be used for kinship inference in forensic practice remains a troubling problem for investigators. Methods: In this study, we selected four popular approaches—KING, IBS, TRUFFLE, and GERMLINE—comprising one method of moment (MoM) estimator and three identical by descent (IBD) segment-based tools and compared their performance at varying numbers of SNPs and levels of genotyping errors using both simulated and real family data. We also explored the possibility of making robust kinship inferences for samples with ultra-high genotyping errors by integrating MoM and the IBD segment-based methods. Results: The results showed that decreasing the number of SNPs had little effect on kinship inference when no fewer than 164 K SNPs were used for all four approaches. However, as the number decreased further, decreased efficiency was observed for the three IBD segment-based methods. Genotyping errors also had a significant effect on kinship inference, especially when they exceeded 1%. In contrast, MoM was much more robust to genotyping errors. Furthermore, the combination of the MoM and the IBD segment-based methods showed a higher overall accuracy, indicating its potential to improve the tolerance to genotyping errors. Conclusions: In conclusion, this study shows that different approaches have unique characteristics and should be selected for different scenarios. More importantly, the integration of the MoM and the IBD segment-based methods can improve the robustness of kinship inference and has great potential for applications in forensic practice.