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European Journal of Human Genetics

Publisher: Nature
Impact Factor: 4.349 (2014)
Years in Print: 1993-present
Journal Website: http://www.nature.com/ejhg/index.html

Articles of Interest

Paternity testing under the cloak of recreational genetics

Journal: European Journal of Human Genetics | Year: 2017

Abstract:

Direct-to-consumer (DTC) internet companies are selling widely advertised and highly popular genetic ancestry tests to the broad public. These tests are often classified as falling within the scope of so-called ‘recreational genetics’, but little is known about the impact of using these services. In this study, a particular focus is whether minors (and under what conditions) should be able to participate in the use of these DTC tests. Current ancestry tests are easily able to reveal whether participants are related and can, therefore, also reveal misattributed paternity, with implications for the minors and adults involved in the testing. We analysed the publicly available privacy policies and terms of services of 43 DTC genetic ancestry companies to assess whether minors are able to participate in testing DTC genetic ancestry, and also whether and how companies ethically account for the potential of paternity inference. Our results indicated that the majority of DTC genetic ancestry testing companies do not specifically address whether minors are able to participate in testing. Furthermore, the majority of the policies and terms of services fail to mention the vulnerability of minors and family members in receiving unexpected information, in particular, in relation to (misattributed) paternity. Therefore, recreational genetics carries both the risk of unintentionally revealing misidentified paternity, and also the risk that fathers will deliberately use these services to test their children’s paternity without revealing their intentions to the mother or any other third party.

Peoples: - | Places: - | Topics: misattributed paternity and NPE | DNA Type: Autosomal DNA, mtDNA, X-DNA, and Y-DNA

Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom

Journal: European Journal of Human Genetics | Year: 2017

Abstract:

Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared with Britons and 800 000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 and 5% (P<2.2 × 10−16). When stratified by their functional annotations, loss-of-function variants showed the highest proportional enrichment in Finns (P=0.0291). In the non-coding part of the genome, variants in conserved regions (P=0.002) and promoters (P=0.01) were also significantly enriched in the Finnish samples. These functional categories represent the highest a priori power for downstream association studies of rare variants using population isolates.

Peoples: Finns | Places: Finland and United Kingdom | Topics: Population isolates and Sequencing Initiative Suomi (SISu) Project | DNA Type: Autosomal DNA

Reconstructing the population history of the largest tribe of India: the Dravidian speaking Gond

Journal: European Journal of Human Genetics | Year: 2017

Abstract:

The Gond comprise the largest tribal group of India with a population exceeding 12 million. Linguistically, the Gond belong to the Gondi–Manda subgroup of the South Central branch of the Dravidian language family. Ethnographers, anthropologists and linguists entertain mutually incompatible hypotheses on their origin. Genetic studies of these people have thus far suffered from the low resolution of the genetic data or the limited number of samples. Therefore, to gain a more comprehensive view on ancient ancestry and genetic affinities of the Gond with the neighbouring populations speaking Indo-European, Dravidian and Austroasiatic languages, we have studied four geographically distinct groups of Gond using high-resolution data. All the Gond groups share a common ancestry with a certain degree of isolation and differentiation. Our allele frequency and haplotype-based analyses reveal that the Gond share substantial genetic ancestry with the Indian Austroasiatic (ie, Munda) groups, rather than with the other Dravidian groups to whom they are most closely related linguistically.

Peoples: Dravidian speakers, Gond, and Manda | Places: India | Topics: Austroasiatic languages, Dravidian languages, and Indo-European languages | DNA Type:

A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data

Journal: European Journal of Human Genetics | Year: 2017

Abstract:

Identical by descent (IBD) segments are used to understand a number of fundamental issues in genetics. IBD segments are typically detected using long stretches of identical alleles between haplotypes in phased, whole-genome SNP data. Phase or SNP call errors in genomic data can degrade accuracy of IBD detection and lead to false-positive/negative calls and to under/overextension of true IBD segments. Furthermore, the number of comparisons increases quadratically with sample size, requiring high computational efficiency. We developed a new IBD segment detection program, FISHR (Find IBD Shared Haplotypes Rapidly), in an attempt to accurately detect IBD segments and to better estimate their endpoints using an algorithm that is fast enough to be deployed on very large whole-genome SNP data sets. We compared the performance of FISHR to three leading IBD segment detection programs: GERMLINE, refined IBD, and HaploScore. Using simulated and real genomic sequence data, we show that FISHR is slightly more accurate than all programs at detecting long (>3 cm) IBD segments but slightly less accurate than refined IBD at detecting short (~1 cm) IBD segments. More centrally, FISHR outperforms all programs in determining the true endpoints of IBD segments, which is crucial for several applications of IBD information. FISHR takes two to three times longer than GERMLINE to run, whereas both GERMLINE and FISHR were orders of magnitude faster than refined IBD and HaploScore. Overall, FISHR provides accurate IBD detection in unrelated individuals and is computationally efficient enough to be utilized on large SNP data sets >60 000 individuals.

Peoples: - | Places: - | Topics: FISHR, GERMLINE, and IBD | DNA Type: Autosomal DNA

Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project

Journal: European Journal of Human Genetics | Year: 2017

Abstract:

Providing ostensibly healthy individuals with personal results from whole-genome sequencing could lead to improved health and well-being via enhanced disease risk prediction, prevention, and diagnosis, but also poses practical and ethical challenges. Understanding how individuals react psychologically and behaviourally will be key in assessing the potential utility of personal whole-genome sequencing. We conducted an exploratory longitudinal cohort study in which quantitative surveys and in-depth qualitative interviews were conducted before and after personal results were returned to individuals who underwent whole-genome sequencing. The participants were offered a range of interpreted results, including Alzheimer’s disease, type 2 diabetes, pharmacogenomics, rare disease-associated variants, and ancestry. They were also offered their raw data. Of the 35 participants at baseline, 29 (82.9%) completed the 6-month follow-up. In the quantitative surveys, test-related distress was low, although it was higher at 1-week than 6-month follow-up (Z=2.68, P=0.007). In the 6-month qualitative interviews, most participants felt happy or relieved about their results. A few were concerned, particularly about rare disease-associated variants and Alzheimer’s disease results. Two of the 29 participants had sought clinical follow-up as a direct or indirect consequence of rare disease-associated variants results. Several had mentioned their results to their doctors. Some participants felt having their raw data might be medically useful to them in the future. The majority reported positive reactions to having their genomes sequenced, but there were notable exceptions to this. The impact and value of returning personal results from whole-genome sequencing when implemented on a larger scale remains to be seen.

Peoples: - | Places: - | Topics: Pharmacogenomics and whole-genome sequencing | DNA Type: Autosomal DNA

Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations

Journal: European Journal of Human Genetics | Year: 2017

Abstract:

Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most recent of the Neolithic samples analyzed in this study 5900 years ago, and identify conditions under which population panmixia between hunter-gatherers/Early-Middle Neolithic farmers and Gurgy cannot be rejected. In relation to other studies on the current debate of the origins of Europeans, these results suggest increasing hunter-gatherer admixture into farmers’ group migrating farther west in Europe.

Peoples: European Neolithic human populations | Places: France | Topics: Neolithic and Neolithic necropolis of Gurgy | DNA Type: mtDNA

Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

Journal: European Journal of Human Genetics | Year: 2016

Abstract:

Recent population genetic studies have provided valuable insights on the demographic history of our species. However, some issues such as the dating of the first demographic expansions in human populations remain puzzling. Indeed, although a few genetic studies argued that the first human expansions were concomitant with the Neolithic transition, many others found signals of expansion events starting during the Palaeolithic. Here we performed a simulation study to show that these contradictory findings may result from the differences in the genetic markers used, especially if two successive expansion events occurred. For a large majority of replicates for each scenario tested, microsatellite data allow only detecting the recent expansion event in that case, whereas sequence data allow only detecting the ancient expansion. Combined with previous real data analyses, our results bring support to the ideas that (i) a first human expansions started during the Palaeolithic period, (ii) a second expansion event occurred later, concomitantly with the Neolithic transition.

Peoples: - | Places: - | Topics: Neolithic and Palaeolithic | DNA Type: Autosomal DNA, mtDNA, and Y-DNA

Lack of gene–language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor

Journal: European Journal of Human Genetics | Year: 2016

Abstract:

Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene–language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene–language correlation in this region. Aiming to investigate gene–language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN- and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixture between the two major linguistic groups had occurred, more so via women than men. Our study therefore provides another example where languages and genes do not conform due to sex-biased genetic admixture across major linguistic groups.

Peoples: | Places: East Timor and Nusa Tenggara | Topics: gene–language relationship | DNA Type: mtDNA and Y-DNA

Mitochondrial cardiomyopathies: how to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny

Journal: European Journal of Human Genetics | Year: 2010

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Characterization of mtDNA variation in a cohort of South African paediatric patients with mitochondrial disease

Journal: European Journal of Human Genetics | Year: 2012

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

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