Chromosome Haplotypes Research Articles

RETRACTED ARTICLE: Y Chromosomal STR haplotypes in Chinese Uyghur, Kazakh and Hui ethnic groups and genetic features of DYS448 null allele and DYS19 duplicated allele.

Y Chromosomal short-tandem repeats (Y-STRs) provide valuable information that can be used for forensic investigation and population studies. The Yfiler® Plus PCR Amplification Kit allows the multiplex amplification of 27 Y-STRs, including seven rapidly mutating markers. With the kit, 447 unrelated males of three minorities (161 Uyghurs, 130 Kazakhs and 156 Huis) from the Xinjiang Uighur Autonomous Region of China were analysed in this study. The gene diversity values of the 27 Y-STRs in the Uyghur, Kazakh and Hui groups ranged from 0.4770 to 0.9545, 0.3897 to 0.9375 and 0.4621 to 0.9725, respectively. One specific sequence pattern of null alleles at the DYS448 locus was confirmed. The individuals carrying the null alleles at the DYS448 locus belonged to haplogroups C2b and C2b1a1b1, while those carrying duplicated alleles at the DYS19 locus belonged to haplogroups C2b1a2 and G2a. A total of 155, 118 and 146 distinct haplotypes were obtained in these three groups, respectively, with overall haplotype diversities of 0.9998, 0.9993 and 0.9996, respectively. Compared with 17 Y-plex, 27 Y-plex demonstrated an increased power of discrimination, especially for the Kazakh group. Visualisation of pairwise genetic distances between 24 ethnic groups in China using multidimensional scaling (MDS) demonstrates the distribution of various groups, which is largely in keeping with ethno-geographic patterns.

Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection

Human migration and trade facilitated domesticated livestock movement, gene flow and development of diverse populations upon which agriculture is based. In addition, varying USA ecological conditions has led to a diverse set of livestock populations to utilize. Quantifying genetic diversity of these populations is incomplete. This paper quantifies genetic diversity captured by the National Animal Germplasm Program and explores genetic structure and differences among 19 pig populations (feral populations from Pacific islands, continental US, and Chinese breeds) using 70,231 SNP from 500 animal samples. Among continental US breeds Fis was consistently low suggesting genetic variability is sufficiently available for breeders to use. A unique population structure using principal component analysis illustrated clear distinctions between Duroc, Yorkshire, Hampshire, breeds of Chinese origin, and feral Pacific Island populations were identified. Five Y chromosome haplotypes were evaluated and demonstrated migration patterns from European, central Asia, and potentially Polynesian waves of gene flow. Quantifying diversity and potential origin of Pacific populations provides insight for future uses, and the need for preservation. Viewing gene bank holdings in context of diversity measures we found a lack of inbreeding within breeds, suggesting the collection represents a wide sampling of individual breeds.

Mitochondrial DNA and Y chromosome-specific polymorphisms in the Seminole Tribe of Florida.

Mitochondrial DNA (mtDNA) sequence variation was examined in 37 Seminoles from Florida by polymerase chain reaction amplification and high resolution restriction endonuclease analysis. The Y chromosome TaqI restriction fragment length polymorphisms detected by the probes 49a, 49f, and 12f2 were examined in the 26 males of this group. Analysis of the mtDNA revealed that all four Native American haplogroups (A, B, C and D) were present in the Seminoles encompassing about 95% of the Seminole mtDNAs. No European mtDNAs were found among the Seminoles, but two mtDNAs (about 5%) were members of the African-specific haplogroup L1, thus indicating that a limited number of African women were incorporated in the Seminole tribe. Analysis of Y chromosome haplotypes supports the hypothesis that haplotypes 18 and 63 are the most likely founding Native American Y chromosome haplotypes from Asia. However, 11% of the Seminole Y chromosomes represented haplotypes generally attributed to Europeans, though none harbored standard African haplotypes. These findings support historical evidence that the Seminole tribe has integrated individuals of European and African ancestry, but suggests that the sex ratio of nonnatives from different continents may have varied.

Forensic and phylogenetic analyses among three Yi populations in Southwest China with 27 Y chromosomal STR loci.

We have analyzed the Y chromosome haplotypes of 510 non-related Yi males grouped in three Chinese provinces (Guizhou, Sichuan, and Yunnan) using the Yfiler® Plus Kit. A total of 484 haplotypes were detected, out of which 460 were unique. The observed haplotype diversity and discrimination capacity were 0.9998 and 0.9490, respectively. To investigate the genetic relationship of the studied population, multidimensional scaling (MDS) plot and neighbor-joining (NJ) tree phylogenetic analyses were constructed which demonstrated that the Y chromosome lineage among the Yi ethnicity was different.

Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits.

The cultivated potato (Solanum tuberosum) has a complex genetic structure due to its autotetraploidy and vegetative propagation which leads to accumulation of mutations and a highly heterozygous genome. A high degree of heterozygosity has been considered to be the main driver of fitness and agronomic trait performance in potato improvement efforts, which is negatively impacted by genetic load. To understand the genetic landscape of cultivated potato, we constructed a gynogenic dihaploid (2n = 2x = 24) population from cv. Superior, prior to development of a high-density genetic map containing 12,753 single nucleotide polymorphisms (SNPs). Common quantitative trait loci (QTL) were identified for tuber traits, vigor and height on chromosomes 2, 4, 7, and 10, while specific QTL for number of inflorescences per plant, and tuber shape were present on chromosomes 4, 6, 10, and 11. Simplex rather than duplex loci were mainly associated with traits. In general, the Q allele (main effect) detected in one or two homologous chromosomes was associated with lower mean trait values suggesting the importance of dosage allelic effects, and the presence of up to two undesired alleles in the QTL region. Loss of heterozygosity has been associated with a lower rate of fitness, yet no correlation between the percent heterozygosity and increased fitness or agronomic performance was observed. Based upon linkage phase, we reconstructed the four homologous chromosome haplotypes of cv. Superior. revealing heterogeneity throughout the genome yet nearly duplicate haplotypes occurring among the homologs of particular chromosomes. These results suggest that the potentially deleterious mutations associated with genetic load in tetraploid potato could be mitigated by multiple loci which is consistent with the theory that epistasis complicates the identification of associations between markers and phenotypic performance.

Abstract 4334: Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer

Abstract Little is known about the genomic features of brain metastases from colorectal cancer (CRC) and the contributing genetic factors. We conducted an analysis of large-scale structural aberrations, including chromosome aneuploidies, with a method called linked-read whole genome sequencing and a new somatic rearrangement detection software tool (ZoomX) to better understand the genomic architecture of brain metastases from CRC. We resolved on average 145 distal inter- and intra-chromosomal somatic junctions per sample with their exact haplotype information and basepair level breakpoints. In addition, we used a new haplotyping method based on these imbalances to generate cancer chromosome haplotypes of up to 146 Mbp long. We identified extensive chromosomal-level instability (CIN) in these cancer genomes, with an average of 90 large-scale copy number aberrations per sample in sizes ranging from hundreds of Kbp to hundreds of Mbp. A substantial fraction of CIN is likely attributable to earlier chromothripsis events. For example, we identified multiple chromothripsis events disrupting the loci of known cancer genes such as TP53, an essential colon cancer driver. We identified novel rearrangements including an oncogenic gene fusion; e.g. SET/DPP10 among these metastatic samples. A majority of chromosome arms demonstrated an allelic imbalance across all of the samples. In summary, the analysis revealed pervasive chromosome-level genome instability as a potential contributor to devastating brain invasion by CRC. It also demonstrated the advantages of linked-read whole genome sequencing. This approach is cost-effective and represents a high-resolution tool to assess genome-wide rearrangements and to generate megabase-scale haplotypes. Citation Format: Li C. Xia, John M. Bell, Christina Wood-Bouwens, Daniel A. King, GiWon Shin, Stephanie Greer, Ian D. Connolly, Melanie H. Gephart, Hanlee P. Ji. Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4334.

Wolf-dog hybridization in Croatia

Wolf-dog hybridization is considered as one of the main threats for wolf conservation since the admixture and introgression of domestic genes may disrupt local adaptations and threaten the long term survival of wild wolf populations. We investigated the occurrence of wolf-dog hybridization in Croatia by analyzing a panel of 12 autosomal microsatellite markers using Bayesian admixture tests, and assessed its directionality by the use of maternally and paternally inherited markers in combination with morphometric data and morphological features. A systematic analysis of morphologic features and morphometric data was used to rank the studied individuals into either phenotypic wild-type wolves or suspected hybrids. By combining Bayesian assignment results with phenotypic features, we set three thresholds which differentiated wolves from hybrids with maximized hybrid detection and a minimized chance for false positive hybrid identification. On the basis of phenotype, out of 176 wild canids, 157 (89.2%) were categorized as wolves and 19 (10.8%) as suspected hybrids. On the basis of the Bayesian admixture tests and phenotype together, five (2.8 percent) animals were classified as wolf-dog hybrids, four of them as backcrosses with wolves, and one as a backcross with a dog. Mitochondrial DNA suggested that all hybrids originated from the mating of female wolves and male dogs. Two male hybrids had Y chromosome haplotypes common to both wolves and dogs, while the other two had wolf private Y chromosome haplotypes. One wolf had a dog Y- haplotype, indicating a past introgression of dog genes. All hybrids were found in Dalmatia, where wolves settled recently, and where they live close to humans, with a high rate of human-caused mortality. These conditions are considered as favorable for wolf- dog hybridization. However, we found a low hybridization prevalence in Croatia, which is nonetheless expected to persist as long as the conditions favoring its occurrence are met. The ecological, sociological, conservation and management implications of hybrid occurrence are yet to be determined.

Transfer of aneuploid embryos following preimplantation genetic diagnosis: the added value of a haplotyping-based genome-wide approach

Introduction: Embryo selection for monogenic diseases has been mainly performed using targeted disease-specific assays. Recently we have developed haplarithmisis, which is based on genomic haplotype reconstruction of cell(s) biopsied from embryos. This provides information not only about the inheritance of Mendelian disease alleles, but also about numerical and structural chromosome anomalies and haplotypes genome-wide. Reflections on how to use this information in the diagnostic laboratory are lacking.

Long range haplotyping of paired-homologous chromosomes by single-chromosome sequencing of a single cell

The longest possible haplotype is chromosome haplotype that is a set of co-inherited alleles occurred on a single strand chromosome inherited from one parent. Standard whole-genome shotgun sequencing technologies are limited by the inability to independently study the haplotype of homologous chromosomes due to the short-reads sequencing strategy and disturbance of homologue chromosomes. Here, we investigated several types of chromosomal abnormalities by a dilution-based method to separate an intact copy of homologous chromosome from human metaphase cells, and then single chromosomes were independently amplified by whole-genome amplification methods, converted into barcoded sequencing libraries, and sequenced in multiplexed pools by Illumina sequencers. We analyzed single chromosome derived from single metaphase cells of one patient with balanced chromosomal translocation t(3;5)(q24;q13), one patient with (47, XXY) karyotype and one with (47, XY, 21+) Down syndrome. We determined the translocation region of chromosomes in patient with t(3;5)(q24;q13) balanced chromosomal translocation by shallow whole-genome sequencing, which is helpful to pinpoint the chromosomal break point. We showed that SCS can physically separate and independently sequence three copies of chromosome 21 of Down syndrome patient. SCS has potential applications in personal genomics, single-cell genomics, and clinical diagnosis, particularly in revealing chromosomal level of genetic diseases.

Insular Celtic population structure and genomic footprints of migration.

Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits.

Distribution of Y chromosomal haplotypes in Japanese native horse populations.

ABSTRACTThe distribution of Y chromosomal haplotypes in Japanese native horse populations was investigated to obtain genetic information on these populations. Here, 159 male/gelded horses from eight local populations were investigated, and three Y haplotypes (JHT-1, JHT-2, and JHT-3) were identified by analyzing five Y-linked loci. Five populations had only JHT-1, whereas two populations had only JHT-2. One population had JHT-1 and JHT-3. Based on the geographical distribution of these haplotypes and previously reported haplotypes for other Asian horses, JHT-1 is considered to be a major haplotype in ancestral native horses. The fixation of each haplotype suggests the influence of independent breeding and genetic drift in each population. These findings complement the results from previous genetic studies of Japanese native horses.

Analysis of degraded casework DNA by redesigning a mini Y-STR multiplex

As partial genetic profile from degraded DNA samples of a case limiting the application of Y-STRs in forensic sciences, a new multiplex mini Y-STR typing was developed to obtain more useful information and complement current commercially available multiplex kits. The multiplex mini Y-STR amplification including three Y-STR loci (DYS385a/b, DYS389 II, and DYS392) was performed to generate amplicons smaller than those of PowerPlex® Y system over 140bp by redesigning primers. Allelic ladders for three mini Y-STR loci were created using a dilution of allelic ladders from the PowerPlex® Y system. A sensitivity test using serially diluted standard 9948 male DNA showed that three mini Y-STR loci were reliable at template concentrations as low as 0.25ng. By comparing of the multiplex mini Y-STR amplification and PowerPlex® Y system with referenced DNA samples, the results indicated stable concordance in genotyping. And then the successful analysis for the degraded DNA samples from the forensic case produced complete genetic profiles with these three loci. So the multiplex mini Y-STR typing combining the aforementioned commercially available kit increased chance of gaining of 16 Y-STR loci profiles within some core loci in Y Chromosome Haplotype Reference Database from forensic casework sample. It is an alternative strategy for recovering locus-specific information from degraded to redesign the suitable mini Y-STR complement besides new commercial Y-STR kits.

Chinese population genetic substructure using 23 Y-chromosomal STRs

China, as the largest national database within the YHRD (Y chromosome haplotype reference database), has repeatedly been a research hotspot in the field of genetics, archaeology and molecular anthropology. In the present study, 23 Y-STR loci were used to investigate genetic relationships among 29 Chinese populations (6029 individuals). Pairwise genetic distance (Rst value) was calculated based on haplotype frequency distributions by the Analysis of Molecular Variance. Multidimensional scaling (MDS) and phylogenetic analysis were performed on the online tool and Mega 6.0, respectively. Tibetans (Rst=0.1601±0.0421), Shuis (Rst=0.0934±0.0327), Uyghurs (Rst=0.0791±0.0459) and Zhuangs (Rst=0.0790±0.0404) showed the high genetic distance with other populations and kept relatively isolated with other reference populations in the MDS plots and Neighbor-Joining tree. Additionally, genetic distinction among same ethnicities (Han and Hui) distributed in different administrative divisions was also explored and no significant differences were identified.

Distribution of the Common or Viviparous Lizard, <i>Zootoca vivipara</i> (Lichtenstein, 1823) (Squamata: Lacertidae) in Central Europe and Re-Colonization of the Baltic Sea Basin: New Karyological Evidence

The widely distributed viviparous lizard Zootoca vivipara (Lichtenstein 1823) revealed considerable differences in physiology, karyology, molecular genetics, and natural history. Based on chromosomal and mtDNA data several distinct karyotypic forms and haplotypes have been described from Central Europe. In an attempt to further clarify the geographic distribution of two karyologically different forms within the viviparous, nominotypic Z. v. vivipara, we studied the karyotypes of specimens from two NE German localities in West Pomerania (Baltic Sea) and Brandenburg, respectively, and also of those from Mt. Kopaonik in Serbia. All individuals karyotyped represented the western form of Z. v. vivipara that differs from other chromosomal forms of Central Europe in several karyotype characters. It inhabits the south coast of the Baltic Sea between the German harbor city of Kiel in the west and the Russian harbor city of Kaliningrad in the east. Recently, the eastern, so-called Russian form of Z. v. vivipara was recorded also in the Kaliningrad exclave, in Belarus near the border Belarus-Poland and even in easternmost Poland, then further eastwards along the Baltic Sea coast including Finland. Our data show that easternmost German populations still belong to the western form, as it is also the case in the SE European Serbian locality sampled. Together with previous data sets, our results document chromosomal uniformity within the western form of Z. v. vivipara from the Baltic Sea coast to the Carpathian basin and the central Balkans, and earlier hypotheses of the postglacial recolonization of the Baltic Sea basin by Z. vivipara are corroborated.

Interaction between Y chromosome haplogroup O3* and 4-n-octylphenol exposure reduces the susceptibility to spermatogenic impairment in Han Chinese

Certain genetic background (mainly Y chromosome haplogroups, Y-hg) may modify the susceptibility of certain environmental exposure to some diseases. Compared with respective main effects of genetic background or environmental exposure, interactions between them reflect more realistic combined effects on the susceptibility to a disease. To identify the interactions on spermatogenic impairment, we performed Y chromosome haplotyping and measurement of 9 urinary phenols concentrations in 774 infertile males and 520 healthy controls in a Han Chinese population, and likelihood ratio tests were used to examine the interactions between Y-hgs and phenols. Originally, we observed that Y-hg C and Y-hg F* might modify the susceptibility to male infertility with urinary 4-n-octylphenol (4-n-OP) level (Pinter = 0.005 and 0.019, respectively). Subsequently, based on our results, two panels were tested to identify the possible protective sub-branches of Y-hg F* to 4-n-OP exposure, and Y-hg O3* was uncovered to interact with 4-n-OP (Pinter = 0.019). In conclusion, while 4-n-OP shows an adverse effect on spermatogenesis, Y-hg O3* makes individuals more adaptive to such an effect for maintaining basic reproductive capacity.

X chromosome drive in a widespread Palearctic woodland fly, Drosophila testacea.

Selfish genes that bias their own transmission during meiosis can spread rapidly in populations, even if they contribute negatively to the fitness of their host. Driving X chromosomes provide a clear example of this type of selfish propagation. These chromosomes have important evolutionary and ecological consequences, and can be found in a broad range of taxa including plants, mammals and insects. Here, we report a new case of X chromosome drive (X drive) in a widespread woodland fly, Drosophila testacea. We show that males carrying the driving X (SR males) sire 80-100% female offspring and possess a diagnostic X chromosome haplotype that is perfectly associated with the sex ratio distortion phenotype. We find that the majority of sons produced by SR males are sterile and appear to lack a Y chromosome, suggesting that meiotic defects involving the Y chromosome may underlie X drive in this species. Abnormalities in sperm cysts of SR males reflect that some spermatids are failing to develop properly, confirming that drive is acting during gametogenesis. By screening wild-caught flies using progeny sex ratios and a diagnostic marker, we demonstrate that the driving X is present in wild populations at a frequency of ~10% and that suppressors of drive are segregating in the same population. The testacea species group appears to be a hot spot for X drive, and D.testacea is a promising model to compare driving X chromosomes in closely related species, some of which may even be younger than the chromosomes themselves.

Forensic characteristics and phylogenetic analysis of Hubei Han population in central China using 17 Y-STR loci

Currently, the largest national database within the Y chromosome haplotype reference database (YHRD, https://yhrd.org, release 53) is China, which has approximately 38000 Y chromosomal 17-marker (Yfiler) haplotypes. These haplotype profiles derived from the vast majority of Chinese administrative divisions, but no haplotype data was available for Hubei province, which is located in the Central China region. Herein, 429 unrelated male Chinese Han individuals residing in Hubei province were recruited and genotyped with 17 Y-STR loci. 115 alleles were identified with corresponding allele frequencies spanned from 0.0023 to 07506. The gene diversity (GD) values ranged from 0.3988 at DYS438 to 0.9573 at DYS385a/b. A total of 410 distinct haplotypes were obtained with the overall haplotype diversity (HD) and discrimination capacity (DC) was 0.9995 and 0.9557, respectively. Additionally, genetic relationships along administrative (Han Chinese from different provinces) and ethnic divisions (minority ethnic groups) were analyzed using analysis of molecular variance (AMOVA) tests and visualized by multidimensional scaling plots (MDS). The Han ethnicity including the Hubei Han shows a high genetic homogeneity all across China and significant genetic differences existed between the Hubei Han and some ethnic groups, most prominently for the Kazakhs and the Tibetans.

A study of the Bodrogköz population in north-eastern Hungary by Y chromosomal haplotypes and haplogroups.

We have determined the distribution of Y chromosomal haplotypes and haplogroups in population samples from one of the most important areas in north-eastern Hungary from many villages in the Bodrogköz. The Bodrogköz region was chosen due to its isolated nature, because this area was a moorland encircled by the Tisza, Bodrog, and Latorca Rivers and inhabitants of this part of Hungary escaped from both Tatar and Ottoman invasions, which decimated the post-Hungarian Conquest populations in many parts of the country. Furthermore, in the first half of the tenth century, this region served as the Palatial Centre and burial grounds of the Hungarian tribes. It has thus been assumed that the present population in this area is likely to be more similar to the population that lived in the Conquest period. We analysed male-specific markers, 23 Y-STRs and more than 30 Y-SNPs, that reflect the past and recent genetic history. We found that the general haplogroup distribution of the samples showed high genetic similarity to non-Bodrogköz Hungarians and neighbouring populations, despite its sheltered location and historical record. We were able to classify the Y-chromosomal haplogroups into four large groups based on STR mutation events: pre-Roman/Roman ancient lineage, Finno-Ugric speakers arriving into the Carpathian Basin, Migration period admixture, and post-Hungarian Conquest admixture. It is clear that a significantly larger database with deep haplogroup resolution, including ancient DNA data, is required to strengthen this research.

Principles guiding embryo selection following genome-wide haplotyping of preimplantation embryos.

How to select and prioritize embryos during PGD following genome-wide haplotyping? In addition to genetic disease-specific information, the embryo selected for transfer is based on ranking criteria including the existence of mitotic and/or meiotic aneuploidies, but not carriership of mutations causing recessive disorders. Embryo selection for monogenic diseases has been mainly performed using targeted disease-specific assays. Recently, these targeted approaches are being complemented by generic genome-wide genetic analysis methods such as karyomapping or haplarithmisis, which are based on genomic haplotype reconstruction of cell(s) biopsied from embryos. This provides not only information about the inheritance of Mendelian disease alleles but also about numerical and structural chromosome anomalies and haplotypes genome-wide. Reflections on how to use this information in the diagnostic laboratory are lacking. We present the results of the first 101 PGD cycles (373 embryos) using haplarithmisis, performed in the Centre for Human Genetics, UZ Leuven. The questions raised were addressed by a multidisciplinary team of clinical geneticist, fertility specialists and ethicists. Sixty-three couples enrolled in the genome-wide haplotyping-based PGD program. Families presented with either inherited genetic variants causing known disorders and/or chromosomal rearrangements that could lead to unbalanced translocations in the offspring. Embryos were selected based on the absence or presence of the disease allele, a trisomy or other chromosomal abnormality leading to known developmental disorders. In addition, morphologically normal Day 5 embryos were prioritized for transfer based on the presence of other chromosomal imbalances and/or carrier information. Some of the choices made and principles put forward are specific for cleavage-stage-based genetic testing. The proposed guidelines are subject to continuous update based on the accumulating knowledge from the implementation of genome-wide methods for PGD in many different centers world-wide as well as the results of ongoing scientific research. Our embryo selection principles have a profound impact on the organization of PGD operations and on the information that is transferred among the genetic unit, the fertility clinic and the patients. These principles are also important for the organization of pre- and post-counseling and influence the interpretation and reporting of preimplantation genotyping results. As novel genome-wide approaches for embryo selection are revolutionizing the field of reproductive genetics, national and international discussions to set general guidelines are warranted. The European Union's Research and Innovation funding programs FP7-PEOPLE-2012-IAPP SARM: 324509 and Horizon 2020 WIDENLIFE: 692065 to J.R.V., T.V., E.D. and M.Z.E. J.R.V., T.V. and M.Z.E. have patents ZL910050-PCT/EP2011/060211-WO/2011/157846 ('Methods for haplotyping single cells') with royalties paid and ZL913096-PCT/EP2014/068315-WO/2015/028576 ('Haplotyping and copy-number typing using polymorphic variant allelic frequencies') with royalties paid, licensed to Cartagenia (Agilent technologies). J.R.V. also has a patent ZL91 2076-PCT/EP20 one 3/070858 ('High throughout genotyping by sequencing') with royalties paid. N/A.

RETRACTED ARTICLE: Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes

China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North-South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.