Genealogical Database Research Articles

Assessment of the quality of genealogical data in breeding enterprises of Western Siberia

Analysis of genealogical databases containing more than 6 million records revealed a significant number of gaps in the data on the origin of animals, especially for sires. This complicates the implementation of automated parental pair selection technologies and reduces the effectiveness of inbreeding level control. It was found that on average 7% of records on ancestors up to the third row of the pedigree contain gaps, of which 85.5% are for sires. This is a serious problem in the creation of regional digital platforms for the automation of decision-making in breeding livestock, limits the possibilities of an objective assessment of the breeding value of animals and hinders the necessary pressure of targeted artificial selection and assignment of sires to breeding stock. Methods for improving the quality of primary genealogical data are proposed, including using foreign sources. It is shown that automation of the decision-making process in purebred dairy breeding allows not only to speed up the detection of errors, but also to significantly reduce the time for their correction thanks to the created data aggregators. This process can become the basis for large-scale verification and validation of primary zootechnical accounting data with subsequent transfer to the Federal State Information and Analytical System of Breeding Resources (FGIAS PR). In addition, this will increase the efficiency of zootechnicians-breeders in large breeding and commercial farms, and will also allow selecting breeding bulls that are genetically compatible with the breeding stock of both a separate region and their totality.

MixDeR: A SNP mixture deconvolution workflow for forensic genetic genealogy.

The generation of forensic DNA profiles consisting of single nucleotide polymorphisms (SNPs) is now being facilitated by wider adoption of next-generation sequencing (NGS) methods in casework laboratories. At the same time, and in part because of this advance, there is an intense focus on the generation of SNP profiles from evidentiary specimens for so-called forensic or investigative genetic genealogy (FGG or IGG) applications. However, FGG methods are constrained by the algorithms for genealogical database searches, which were designed for use with single-source profiles, and the fact that many forensic samples are mixtures. To enable the use of two-person mixtures for FGG, we developed a workflow, MixDeR, for the deconvolution of mixed SNP profiles. MixDeR, a flexible and easy to use R package and Shiny app, processes ForenSeq Kintelligence® (QIAGEN, Inc.) SNP genotyping results and directs deconvolution of the profiles in EuroForMix (EFM). MixDeR then filters the EFM outputs to produce inferred single-source genotypes in reports formatted for use with GEDmatch® PRO. An optional MixDeR output includes metrics that assist with testing and validation of the workflow. As the Shiny app provides a graphical user interface and the software is designed to be run offline, MixDeR should be suitable for use by any laboratory developing FGG capabilities, no matter their bioinformatic resources or expertise.

Familial risk and phenotypic variation of sarcoidosis in the Icelandic population

BackgroundThe familial risk of sarcoidosis is heterogeneous, previous studies demonstrate conflicting results. The present study maps the pattern of familial distribution of all known, biopsy-verified sarcoidosis in the Icelandic population (1981–2021).MethodsAll cases were re-confirmed and categorized into one of the five phenotypic groups described by Schuppet al., and in different groups based on disease severity. Distant relationships were accurately traced for relatives of sarcoidosis patients and their mates using the nationwide Icelandic Genealogy Database. This allows creation of matched control groups for the calculation of Relative Risk (RR) and Kinship Coefficient (KC).Results462 patients with biopsy-proven diagnoses of sarcoidosis were included. We identified 282 extended families and seven sibling pairs with sarcoidosis. Twenty families had five or more affected individuals. RR was 3.7 (95%CI: 1.54–8.55) in 1st-degree relatives (p=0.003), 1.65 (1.05–1.92) in 4th-degree relatives, (p=0.014) and 1.57 (1.08–1.70) in 5th-degree relatives (p=0.003). RRs among 1st-5th degree relatives of the patients’ mates were not significant. KC for sarcoidosis was only significant for the first two meiosis (KC=1.06, p<0.008 and KC=1.01, p=0.011, respectively). The most common sarcoidosis phenotypes were pulmonary-lymphonodal (47.6%), ocular-cardiac-cutaneous and central nervous system (OCCC) (21.6%), and musculoskeletal cutaneous (MSC) (20.9%). There seems to be no clustering of a single phenotype or resistant sarcoidosis in the extended sarcoidosis families.ConclusionOur study does not consider heritability a strong risk factor for sarcoidosis. The risk is highest for first-degree relatives of patients with sarcoidosis. Single phenotypes and resistant sarcoidosis do not cluster in distinct families.

FIGG at 5: An update on U.S. public perspectives on forensic investigative genetic genealogy five years after its introduction to criminal investigations.

In 2018, after law enforcement announced it had used a technique called forensic investigative genetic genealogy (FIGG) to identify the Golden State Killer, we conducted a U.S. general population survey and found most respondents supported using FIGG to solve violent crimes. Since then, FIGG has helped close hundreds of criminal cases, but it also has weathered controversies. On FIGG's fifth anniversary, we conducted an expanded, follow-up survey with U.S.-based participants to determine if public opinion had changed and found continued support for FIGG across most applications. The same proportion (91 %) of respondents in the 2018 and 2023 surveys endorsed using FIGG in genetic genealogy databases to help identify perpetrators of violent crimes. Similar to the 2018 survey, only 57 % of respondents supported FIGG to help identify perpetrators of non-violent crimes. The results indicate that U.S. policies that have been adopted for FIGG are generally consistent with the opinions of our survey respondents over time. Nonetheless, there are opportunities to strengthen FIGG governance with the goal of maintaining public trust in the technique.

Investigative genetic genealogy practices warranting policy attention: Results of a modified policy Delphi.

A technique known as investigative genetic genealogy (IGG) was first introduced to criminal investigations in 2018, and it has since been used by U.S. law enforcement to help identify hundreds of criminal perpetrators and unidentified human remains. As expertise in IGG grows, policymakers have shown interest in regulating it. To help inform these efforts and to promote coherence in IGG governance as it expands, we recruited experts representing a spectrum of IGG-relevant professions and perspectives to identify and prioritize IGG practices for policy attention and to develop policy options for addressing them. In two rounds of a modified policy Delphi, 31 participants prioritized nine IGG practices for policy attention. These top priority practices relate to: consent and notification; case eligibility and criteria; data management, privacy, and security; and governance and accountability. Participants expressed a range of opinions, some strongly held, and did not reach complete consensus with respect to any of the practices. However, convergence was strongest with respect to law enforcement participation in direct-to-consumer genetic genealogy databases against terms of service, which a large majority opposed and almost half evaluated as top priority for policy attention. Participants also voiced strong and consistent concern about management of data and samples collected and generated during IGG and the governance of private laboratories involved in IGG. Our study demonstrates the feasibility and value of engaging with diverse experts over an extended period on a pressing matter of public policy and provides a needed empirical foundation for IGG policymaking.

Ghosts in the Machine: Possessive Selves, Inert Kinship, and the Potential Whiteness of “Genealogical” Indigeneity

This article explores the recent rise in the use of self-identification as a key element of legitimacy in contemporary claims to Indigeneity. Emphasizing self-identification as a central dynamic of all identity-making in contemporary nation-states, the article argues nonetheless that this element of identity is insufficient for making ethical claims to Indigeneity. Emphasizing instead the importance of ongoing Indigenous relationality (i.e., kinship), it argues that genealogical databases potentially exacerbate the potential to engage in non-relational forms of belonging that undermine Indigenous communities’ and nations’ autonomy in defining the boundaries and contours of their citizenship. I undertake this argument in three broad parts. Part one undertakes a selective discussion of sociologist Stuart Hall’s conceptualization of identity, highlighting what I regard as two relevant elements key to his identity-making framework. Part two then undertakes a brief discussion of Geonpul scholar Aileen Moreton-Robinson’s discussion of white possessiveness as a useful lens for framing the growing self-Indigenization/Pretendianism literature as variegated examples of analyzing its practice; and finally, part three explores the potential of genealogical databases to encourage possessive/non-relational forms of identity-making, what I term here “inert kinship”. The article then concludes with a brief discussion regarding how genealogical databases might be used ethically with respect to claiming Indigenous belonging, and why this is key to the upholding of Indigenous sovereignty.

Molecular Pathology of Myotonic Dystrophy Type 1 in Iceland.

Myotonic Dystrophy type 1 (DM1) is an autosomal dominant disease with anticipation due to increased number of CTG repeats in the DMPK gene. This retrospective, cohort study in Iceland assessed prevalence of DM1, molecular pathology, and patient ascertainment. Data was collected from all major hospitals in Iceland, Medical Director of Health, and independent clinics. Cohort criteria were diagnosis of DM1 on January 1, 2021, or time of death. Population-based Icelandic Genealogy Database of the Genetical Committee at the University of Iceland was used for genealogy. In Iceland, 221 individuals, including 19 obligate carriers, had been diagnosed with DM1 of which 144 were alive giving a point prevalence of 39 per 100,000 (four times the world average of 9.3). Genealogy analysis identified 45 first-degree families. Age-adjusted prevalence ranged between 11 and 66 per 100,000. Average potential years of life lost were 20.5 per person. Where information was available, 63% of ascertainment was based on family history in cascade testing. The differences in age-adjusted prevalence suggest that the overall point prevalence is an underestimation due to underdiagnosis in younger age groups and lethality in oldest age group. Our data supports use of cascade testing to improve DM1 ascertainment.

It’s all relative: A multi-generational study using ForenSeq™ Kintelligence

The successful application of Forensic Investigative Genetic Genealogy (FIGG) to the identification of unidentified human remains and perpetrators of serious crime has led to a growing interest in its use internationally, including Australia. Routinely, FIGG has relied on the generation of high-density single nucleotide polymorphism (SNP) profiles from forensic samples using whole genome array (WGA) (∼650,000 or more SNPs) or whole genome sequencing (WGS) (millions of SNPs) for DNA segment-based comparisons in commercially available genealogy databases. To date, this approach has required DNA of a quality and quantity that is often not compatible with forensic samples. Furthermore, it requires the management of large data sets that include SNPs of medical relevance. The ForenSeq™ Kintelligence kit, comprising of 10,230 SNPs including 9867 for kinship association, was designed to overcome these challenges using a targeted amplicon sequencing-based method developed for low DNA inputs, inhibited and/or degraded forensic samples. To assess the ability of the ForenSeq™ Kintelligence workflow to correctly predict biological relationships, a comparative study comprising of 12 individuals from a family (with varying degrees of relatedness from 1st to 6th degree relatives) was undertaken using ForenSeq™ Kintelligence and a WGA approach using the Illumina Global Screening Array-24 version 3.0 Beadchip. All expected 1st, 2nd, 3rd, 4th and 5th degree relationships were correctly predicted using ForenSeq™ Kintelligence, while the expected 6th degree relationships were not detected. Given the (often) limited availability of forensic samples, findings from this study will assist Australian Law enforcement and other agencies considering the use of FIGG, to determine if the ForenSeq™ Kintelligence is suitable for existing workflows and casework sample types considered for FIGG.

“The truth should not be hidden”: Experiences and recommendations of individuals making NPE discoveries through genetic genealogy databases

PurposeFueled by direct-to-consumer (DTC) genetic testing and genetic-relative finder services, some participants in genetic genealogy databases are making “not parent expected” (NPE) discoveries. To better understand experiences of this phenomenon, we surveyed a large cohort of users of genetic relative finder (GRF) services concerning their experiences after an NPE discovery. MethodsUsing thematic analysis, we analyzed responses from a cohort of GRF users (n = 646) to open-ended survey items to understand these experiences and their recommendations for DTC genetic testing companies and other GRF users. ResultsWe found that individuals had both positive and negative emotional experiences related to the NPE discovery. Positive aspects included deeper self-understanding, connecting with new family members, and uncovering answers to questions. Negative aspects included rejection by new genetic relatives, inability to seek answers from relatives who had already died, and impairment of family relationships, especially with mothers. For many participants, the challenges after the discovery nevertheless felt worthwhile because the truth was uncovered. Perhaps notably, some participants suggested enhanced warnings prediscovery and improved support after discovery from companies who provide DTC genetic testing services. ConclusionGRF services are powerful tools for family research and genealogy. Despite some possible positive and worthwhile experiences arising from making an NPE discovery, GRF users risk dealing with this potentially life-altering experience without adequate support. Participants in this study recommended an increase in resources from DTC genetic testing companies that could help users anticipate and navigate an NPE discovery.

Forensic genetics in the shadows

Abstract This article examines the controversial practice of law enforcement agencies searching genetic samples obtained in health care settings, without a warrant or consent. While police have previously used public genealogy databases for this purpose, our article describes how they are now secretly accessing genetic information from newborn screening programs and medical tests. This raises ethical and legal concerns, blurring the line between health care and law enforcement. This, in turn, may discourage people from seeking important medical care due to distrust in the police and privacy concerns. To explore public attitudes on this issue, the authors conducted a study examining how lay people view the forensic use of clinical genetic data for different types of crimes. Our findings suggest that people take a utilitarian perspective, where they are more likely to support warrantless searches for serious and ongoing crimes but more likely to oppose these searches for more minor offenses like theft. However, regardless of public support, the little-known practice undermines trust in health care institutions and violates patient privacy. We recommend three legal reforms to restrict law enforcement access to clinical and public health genetic databases and to require explicit consent to forensic uses.

Genealogical Ethics in the United States and the Popularization of Genealogical Research in the Digital Age

This article examines genealogical ethics in the digital age. At a time when more resources for research are available digitally than ever previously, digital media also pose challenges for the large-scale dissemination of false or misleading information as well as the incautious presentation of more careful research that then might be misconstrued by some. This article first reviews the literature about the development of academic genealogy and professional ethical standards. It then provides a series of case studies, each of which examines particular situations in which ethical questions have arisen about the presentation of research findings. This article argues for a greater need among lay researchers to pursue careful research and for a greater need among commercial genealogical databases to foster that. It also argues for the need, grounded in the ethical respect for human dignity, to recognize the individuality and to respect the dignity of the life stories of those whom we study and about whom we write, which should undergird the research process and the presentation of findings. In a concluding section, this essay presents several suggestions that could be used by commercial genealogical companies and researchers to promote more careful investigation and to improve the presentation of findings in commercial databases, online trees, genealogical websites, and other genealogical works that do not routinely undergo peer review.

Trends in assortative mating in the United States, 1700–1910. Evidence from FamiLinx data

ABSTRACT Couple formation and assortative mating significantly influence societal structures, as marriages between individuals from diverse geographical or social backgrounds promote intra-family diversity. Understanding these patterns is crucial for grasping the demographic processes that shape contemporary societies. However, the scarcity of comprehensive data has impeded progress in this area. This paper aims to fill this gap by investigating assortative mating trends in the United States among birth cohorts from 1700 to 1910, utilizing data from FamiLinx, an online crowdsourced genealogical database. We focus on two primary dimensions: migration background (including natives, first and second-generation migrants) and age at marriage. Our analysis yields three major findings. First, we document significant changes in assortative mating trends over time, reflecting the dynamic nature of mate selection and its responsiveness to societal shifts. Second, we uncover substantial heterogeneity in assortative mating patterns across different social groups, indicating varying social dynamics and preferences. Third, we illustrate how these trends can be differently interpreted depending on whether the perspective is individual or familial. Additionally, we explore the advantages and limitations of using online genealogical data for historical studies of assortative mating, highlighting its potential for offering new insights while acknowledging the challenges posed by data quality and representativeness.

The Effect of Increased Latin American Representation in Investigative Genetic Genealogy Databases on Unidentified Remains Cases

The Effect of Increased Latin American Representation in Investigative Genetic Genealogy Databases on Unidentified Remains Cases

Public Perspectives on Investigative Genetic Genealogy: Findings from a National Focus Group Study

Background Investigative genetic genealogy (IGG) is a technique that involves uploading genotypes developed from perpetrator DNA left at a crime scene, or DNA from unidentified remains, to public genetic genealogy databases to identify genetic relatives and, through the creation of a family tree, the individual who was the source of the DNA. As policymakers demonstrate interest in regulating IGG, it is important to understand public perspectives on IGG to determine whether proposed policies are aligned with public attitudes. Methods We conducted eight focus groups with members of the public (N = 72), sampled from four geographically diverse US regions, to explore general attitudes and perspectives regarding aspects of IGG practices, applications, and policies. Five major topics were explored in each focus group: when IGG should be used; who should perform IGG; how to approach consent for genetic database users; what systems of oversight should govern IGG practitioners; and whether to notify database users if their data are involved in law enforcement (LE) matching. Results Participants were supportive of IGG in most scenarios, especially for cold and violent cases. The favorable attitudes toward IGG were, however, tempered by distrust of law enforcement among some participants. All participants agreed that databases must inform users if IGG is allowed, but they did not agree on how individual database users should be allowed to opt out or whether to notify them if their data are involved in specific investigations. All participants agreed that IGG should be subject to some prescriptive guidelines, regulations, or accountability mechanisms. Conclusions These findings suggest broad public support for IGG, and interest in developing systems of accountability for its practice. Our study provides useful insight for policy makers, genomic database stewards, law enforcement, and other stakeholders in IGG’s practice, and suggests multiple directions for future research.

IGG in the trenches: Results of an in-depth interview study on the practice, politics, and future of investigative genetic genealogy

Investigative genetic genealogy (IGG) is a new technique for identifying criminal suspects and unidentified deceased and living persons that has sparked controversy. In a criminal case, the technique involves uploading genetic information left by a putative perpetrator at the crime scene to one or more direct-to-consumer genetic genealogy databases with the intention of identifying the perpetrator's genetic relatives and, eventually, locating the perpetrator on the family tree. In 2018, IGG helped to identify the Golden State Killer, and it has since been used in hundreds of investigations in the United States. Here, we report findings from in-depth interviews with 24 U.S.-based individuals involved in IGG that are relevant to the technique’s current practice and predicted future. Key findings include: an emphasis on restricting IGG as a conceptual and technical matter to lead generation; the rapid growth of a private and largely self-regulating industry to support IGG; general recognition of three categories of cases associated with distinct practical, ethical, and policy questions, as well as varying degrees of controversy; and the significant influence of perceived public opinion on IGG practice. The experiences and perspectives of individuals in the IGG trenches related to these and other issues are potentially useful inputs to ongoing efforts to regulate the technique.

Web-based information system framework for the digitization of historical databases and endowments

With the digitization of historical databases and endowments, care must be taken when designing the framework for an information system on the web. Because conflicts arise frequently in reality, different data management requirements are necessary for the preservation of waqf property. For the purpose of creating and putting into place historical information systems and endowments for this inheritance, it is necessary to develop an acceptable management plan. An inheritance that is thought to be distinct from customary ones since it is governed by its own law is referred to as waqf, as an example. They typically comprise histories and endowments that need to be protected to ensure sustenance among the population and to ensure they live up to the standards of the community and country. This research was compiled and analyzed to support stakeholders in producing a more practical, focused, and value-delivery framework. The datasets were mapped based on relationships, graph databases, and semantic networks. Moreover, the framework was developed using several data representation models to ensure easier, faster, and more accurate methods of displaying the data. Relationships, graph databases, and semantic networks were used to map the datasets. The design was made available to users, administrators, and managers, with the latter group being in charge of maintaining data control over each entity. The case study was conducted using historical information and waqf from the Nadzir Pangeran Sumedang Indonesia Waqf Foundation (YNWPS) in the Kingdom of Sumedang Larang Indonesia (KSL).` The creation of a web-based information system to keep track of the data in each entity and ensure better preservation of historical genealogical databases and endowments was made simpler by the structured framework design.

Law enforcement use of genetic genealogy databases in criminal investigations: Nomenclature, definition and scope

Although law enforcement use of commercial genetic genealogy databases has gained prominence since the arrest of the Golden State Killer in 2018, and it has been used in hundreds of cases in the United States and more recently in Europe and Australia, it does not have a standard nomenclature and scope. We analyzed the more common terms currently being used and propose a common nomenclature: investigative forensic genetic genealogy (iFGG). We define iFGG as the use by law enforcement of genetic genealogy combined with traditional genealogy to generate suspect investigational leads from forensic samples in criminal investigations. We describe iFGG as a proper subset of forensic genetic genealogy, that is, FGG as applied by law enforcement to criminal investigations; hence, investigative FGG or iFGG. We delineate its steps, compare and contrast it with other investigative techniques involving genetic evidence, and contextualize its use within criminal investigations. This characterization is a critical input to future studies regarding the legal status of iFGG and its implications on the right to genetic privacy.

Protecting Genetic Genealogical Databases from Identical-by-State Probing Attacks: A Machine Learning-Based Approach

Identical-by-state (IBS) probing is a way of attacking a public genealogy database to discover the identities of people who share specific qualities. The attacker creates an IBS-inert DNA sequence (IBS-inert-DNA-sequence) and combines it with a sequence containing the trait of interest. The final sequence matches people with genomic areas similar to the trait. To prevent attacks, it was hypothesized that the design of IBS-inert-DNA-sequences is based on the principle that they are susceptible to detection by skilled machine learning systems, because the attacker purposely creates an IBS-inert-DNA-sequence which is structurally dissimilar to real DNA sequences. The dataset consisted of real DNA (from the UCI Machine Learning Repository's splice junction gene sequences dataset) and computer-generated sequences. Eighteen non-identical Random Forest classifier models (RF-models) were created to determine the best configurations for discriminating between real and computer-generated sequences. The findings revealed that an optimized RF-model combined with k-mer and n-gram values of 2 each, resulted in the most performant model, with accuracy, sensitivity, specificity, false positive rate, Matthew’s correlation coefficient, and area under the receiver operating characteristic curve values of 88.3%, 84.8%, 91.8%, 8.2%, 0.768 and 0.958, respectively. A decline in performance was linked to an increase in k-mer size.

Legacies of Legibility: Genealogical Story-Telling as an Echo of State Power

Genealogy necessitates historical records, the majority of which derive from government sources, despite families’ “private” lives. State records weren’t intended to service future family historians, but were a means to state-formation and power. Consequently, records used by family historians reflect statist concerns, not state subjects’. Genealogy databases and censuses were analyzed to determine how many derive from state sources. An individual, anecdotal example focused upon a US Census record illuminates genealogical insight and misunderstanding; despite relevance, interpretation problems confront family historians. Genealogical research is limited by modernity's governmentality and the state gaze, impacts generally under-acknowledged by the average family historian.

Analysis of acute extremity compartment syndrome using a genealogic population database.

Acute extremity compartment syndrome ("CS") is an under-researched, highly morbid condition affecting trauma populations. The purpose of this study was to analyze incidence rates and risk factors for extremity compartment syndrome using a high-quality population database. Additionally, we evaluated heritable risk for CS using available genealogic data. We hypothesized that diagnosis of extremity compartment syndrome would demonstrate heritability. Adult patients with fractures of the tibia, femur, and upper extremity were retrospectively identified by ICD-9, ICD-10, and CPT codes from 1996 to 2020 in a statewide hospital database. Exposed and unexposed cohorts were created based on a diagnosis of CS. Available demographic data were analyzed to determine risk factors for compartment syndrome using logistic regression. Mortality risk at the final follow-up was evaluated using Cox proportional hazard modeling. Patients with a diagnosis of CS were matched with those without a diagnosis for heritability analysis. Of 158,624 fractures, 931 patients were diagnosed with CS. Incidence of CS was 0.59% (tibia 0.83%, femur 0.31%, upper extremity 0.27%). Male sex (78.1% vs. 46.4%; p < 0.001; RR = 3.24), younger age at fracture (38.8 vs. 48.0years; p < 0.001; RR = 0.74), Medicaid enrollment (13.2% vs. 9.3%; p < 0.001; RR = 1.58), and smoking (41.1% vs. 31.1%; p < 0.001; RR 1.67) were significant risk factors for CS. CS was associated with mortality (RR 1.61, p < 0.001) at mean follow-up 8.9years in the CS cohort. No significant heritable risk was found for diagnosis of CS. Without isolating high-risk fractures, rates of CS are lower than previously reported in the literature. Male sex, younger age, smoking, and Medicaid enrollment were independent risk factors for CS. CS increased mortality risk at long-term follow-up. No heritable risk was found for CS. III.