ABO Genetic Variation in Neanderthals and Denisovans

Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications

Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.

Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants

In the era of blood group genomics, reference collections of complete and fully resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (ie, separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully resolved sequences for all 6 main ABO allele groups: ABO∗A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype data set (n = 25 200) of serologically typed Swiss blood donors. The entire ABO gene was amplified in 2 overlapping long-range polymerase chain reactions (covering ∼23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, 2 samples per ABO group were resequenced using Illumina and Pacific Biosciences technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered 4 genetic variants putatively specific for ABO∗A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n = 4872) of a multiethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.

Association of ABO blood groups with ovarian reserve: a retrospective cohort study in Chinese Han women younger than 40 years with infertility

BACKGROUND

Ovarian reserve reflects both the quantity and quality of oocytes available for procreation and is affected by many known and unknown factors. ABO blood type is related to several infertility processes, but it is unclear whether and how ABO blood type affects ovarian reserve.

OBJECTIVE

The purpose of the study was to explore the correlation between ABO blood types and ovarian reserve in infertile Chinese Han women under 40 years of age undergoing the in vitro fertilization (IVF)/ intracytoplasmic sperm injection (ICSI)-embryo transfer (IVF/ICSI-ET) treatment.

METHODS

Women aged < 40 years who underwent IVF/ICSI-ET at our institution and had a documented ABO blood type were eligible for this study. In this study, patients were divided into two groups according to the diminished ovarian reserve (DOR) group (AMH < 1.1 ng/mL, AFC < 6) and the non-diminished ovarian reserve (non-DOR) group (AMH ≥ 1.1 ng/mL, AFC ≥ 6). The relationship between ovarian reserve and ABO blood group was determined by correlation analysis.

RESULTS

In this retrospective cohort study, clinical data were collected from 1690 Chinese Han women treated with IVF/ ICSI-ET in hospital records between April 2019 and March 2020 in the affiliated hospital of Southwest Medical University, located in Luzhou, China. The differences in age, duration of infertility, BMI, FSH, FSH / LH, and p (DOR vs non-DOR) for each parameter (DOR vs non-DOR) were statistically significant, and the differences in LH and E2 were not statistically significant. ABO blood groups were most prevalent in the DOR group with O (143, 34.8%) and A (122, 29.7%) and in the non-DOR group with A (428, 33.5%) and O (419, 32.8%). ABO blood groups were most prevalent in the DOR group with O (n = 57, 30.5%) and A (n = 54, 28.9%) and in the non-DOR group with A (n = 335, 34.0%) and O (n = 323, 32.8%) were the most frequent in the non-DOR group.

CONCLUSIONS

In this retrospective cohort study, we confirmed the lack of a significant association between ABO blood type and ovarian reserve. Further studies are needed to clarify whether there is any prognostic correlation between ABO blood group and ovarian reserve in women undergoing IVF/ICSI-ET.

Apportioning archaic variants among modern populations

The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives. Resolving the interactions between modern and archaic human populations can be difficult, as archaic variants in modern populations have been shaped by genetic drift, bottlenecks and gene flow. Here, we investigate the distribution of archaic variation in Eurasian populations. We find that archaic ancestry coverage at the individual- and population-level present distinct patterns in modern human populations: South Asians have nearly twice the number of population-unique archaic alleles compared with Europeans or East Asians, indicating that these populations experienced differing demographic and archaic admixture events. We confirm previous observations that East Asian individuals have more Neanderthal ancestry than European individuals, but surprisingly, when we compare the number of single nucleotide polymorphisms with archaic alleles found across a population, Europeans have more Neanderthal ancestry than East Asians. We compare these results to simulated models and conclude that these patterns are consistent with multiple admixture events between modern humans and Neanderthals.

This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.