Recombination map tailored to Native Hawaiians may improve robustness of genomic scans for positive selection

Recombination events establish the patterns of haplotypic structure in a population and estimates of recombination rates are used in several downstream population and statistical genetic analyses. Using suboptimal maps from distantly related populations may reduce the efficacy of genomic analyses, particularly for underrepresented populations such as the Native Hawaiians. To overcome this challenge, we constructed recombination maps using genome-wide array data from two study samples of Native Hawaiians: one reflecting the current admixed state of Native Hawaiians (NH map) and one based on individuals of enriched Polynesian ancestries (PNS map) with the potential to be used for less admixed Polynesian populations such as the Samoans. We found the recombination landscape to be less correlated with those from other continental populations (e.g. Spearman's rho = 0.79 between PNS and CEU (Utah residents with Northern and Western European ancestry) compared to 0.92 between YRI (Yoruba in Ibadan, Nigeria) and CEU at 50 kb resolution), likely driven by the unique demographic history of the Native Hawaiians. PNS also shared the fewest recombination hotspots with other populations (e.g. 8% of hotspots shared between PNS and CEU compared to 27% of hotspots shared between YRI and CEU). We found that downstream analyses in the Native Hawaiian population, such as local ancestry inference, imputation, and IBD segment and relatedness detections, would achieve similar efficacy when using the NH map compared to an omnibus map. However, for genome scans of adaptive loci using integrated haplotype scores, we found several loci with apparent genome-wide significant signals (|Z-score|> 4) in Native Hawaiians that would not have been significant when analyzed using NH-specific maps. Population-specific recombination maps may therefore improve the robustness of haplotype-based statistics and help us better characterize the evolutionary history that may underlie Native Hawaiian-specific health conditions that persist today.

A likelihood-based framework for demographic inference from genealogical trees

The demographic history of a population drives the pattern of genetic variation and is encoded in the gene-genealogical trees of the sampled alleles. However, existing methods to infer demographic history from genetic data tend to use relatively low-dimensional summaries of the genealogy, such as allele frequency spectra. As a step toward capturing more of the information encoded in the genome-wide sequence of genealogical trees, here we propose a novel framework called the genealogical likelihood (gLike), which derives the full likelihood of a genealogical tree under any hypothesized demographic history. Employing a graph-based structure, gLike summarizes across independent trees the relationships among all lineages in a tree with all possible trajectories of population memberships through time and efficiently computes the exact marginal probability under a parameterized demographic model. Through extensive simulations and empirical applications on populations that have experienced multiple admixtures, we showed that gLike can accurately estimate dozens of demographic parameters when the true genealogy is known, including ancestral population sizes, admixture timing, and admixture proportions. Moreover, when using genealogical trees inferred from genetic data, we showed that gLike outperformed conventional demographic inference methods that leverage only the allele-frequency spectrum and yielded parameter estimates that align with established historical knowledge of the past demographic histories for populations like Latino Americans and Native Hawaiians. Furthermore, our framework can trace ancestral histories by analyzing a sample from the admixed population without proxies for its source populations, removing the need to sample ancestral populations that may no longer exist. Taken together, our proposed gLike framework harnesses underutilized genealogical information to offer exceptional sensitivity and accuracy in inferring complex demographies for humans and other species, particularly as estimation of genome-wide genealogies improves.

Recombination map tailored to Native Hawaiians improves robustness of genomic scans for positive selection

Recombination events establish the patterns of haplotypic structure in a population and estimates of recombination rates are used in several downstream population and statistical genetic analyses. Using suboptimal maps from distantly related populations may reduce the efficacy of genomic analyses, particularly for underrepresented populations such as the Native Hawaiians. To overcome this challenge, we constructed recombination maps using genome-wide array data from two study samples of Native Hawaiians: one reflecting the current admixed state of Native Hawaiians (NH map), and one based on individuals of enriched Polynesian ancestries (PNS map) with the potential to be used for less admixed Polynesian populations such as the Samoans. We found the recombination landscape to be less correlated with those from other continental populations (e.g. Spearman's rho = 0.79 between PNS and CEU (Utah residents with Northern and Western European ancestry) compared to 0.92 between YRI (Yoruba in Ibadan, Nigeria) and CEU at 50 kb resolution), likely driven by the unique demographic history of the Native Hawaiians. PNS also shared the fewest recombination hotspots with other populations (e.g. 8% of hotspots shared between PNS and CEU compared to 27% of hotspots shared between YRI and CEU). We found that downstream analyses in the Native Hawaiian population, such as local ancestry inference, imputation, and IBD segment and relatedness detections, would achieve similar efficacy when using the NH map compared to an omnibus map. However, for genome scans of adaptive loci using integrated haplotype scores, we found several loci with apparent genome-wide significant signals (|Z-score| > 4) in Native Hawaiians that would not have been significant when analyzed using NH-specific maps. Population-specific recombination maps may therefore improve the robustness of haplotype-based statistics and help us better characterize the evolutionary history that may underlie Native Hawaiian-specific health conditions that persist today.

The impact of global and local Polynesian genetic ancestry on complex traits in Native Hawaiians

Epidemiological studies of obesity, Type-2 diabetes (T2D), cardiovascular diseases and several common cancers have revealed an increased risk in Native Hawaiians compared to European- or Asian-Americans living in the Hawaiian islands. However, there remains a gap in our understanding of the genetic factors that affect the health of Native Hawaiians. To fill this gap, we studied the genetic risk factors at both the chromosomal and sub-chromosomal scales using genome-wide SNP array data on ~4,000 Native Hawaiians from the Multiethnic Cohort. We estimated the genomic proportion of Native Hawaiian ancestry ("global ancestry," which we presumed to be Polynesian in origin), as well as this ancestral component along each chromosome ("local ancestry") and tested their respective association with binary and quantitative cardiometabolic traits. After attempting to adjust for non-genetic covariates evaluated through questionnaires, we found that per 10% increase in global Polynesian genetic ancestry, there is a respective 8.6%, and 11.0% increase in the odds of being diabetic (P = 1.65×10-4) and having heart failure (P = 2.18×10-4), as well as a 0.059 s.d. increase in BMI (P = 1.04×10-10). When testing the association of local Polynesian ancestry with risk of disease or biomarkers, we identified a chr6 region associated with T2D. This association was driven by an uniquely prevalent variant in Polynesian ancestry individuals. However, we could not replicate this finding in an independent Polynesian cohort from Samoa due to the small sample size of the replication cohort. In conclusion, we showed that Polynesian ancestry, which likely capture both genetic and lifestyle risk factors, is associated with an increased risk of obesity, Type-2 diabetes, and heart failure, and that larger cohorts of Polynesian ancestry individuals will be needed to replicate the putative association on chr6 with T2D.

Generation of monoclonal antibodies reactive with nuclear proteins of human primary breast tumors

Nuclear proteins were extracted from purified nuclei of human primary breast tumors (BrT) and bladder tumors and of human normal breast, kidney and lymphocytes by enzymatic treatment. SDS-Polyacrylamide gel electrophoresis of nuclear proteins from breast tumors showed different bands in the molecular weight zones from 25 to 220 kDa which were absent or present only as traces in normal breast tissue. Murine monoclonal antibodies (MAbs) have been produced using nuclear extracts of human primary breast tumors as immunogens. Approximately 2,000 hybridomas were generated from 5 hybridizations. According to their reactivity to BrT nuclear extracts and mammary carcinoma cell line MCF-7, seven hybridomas were selected and cloned. They were further characterized with histological immunoperoxidase assays of formaldehyde-fixed BrT paraffin tissue sections. MAb 6A3 particularly gave strong nuclear staining with all BrT specimens while MAb 1D8 showed both nuclear and cytoplasmic staining with only some of them. Specimens from mammoplasty did not react with these MAbs. Immunoblotting of BrT nuclear extracts as developed with MAbs 6A3 and 1D8 revealed major protein bands with molecular weight of 120 and 130 kDa. The potential use of these MAb-defined BrT-related nuclear proteins as markers for human breast cancer was suggested.

Comparison of nuclear proteins from DMBA-induced mammary tumors and lactating mammary glands by polyacrylamide gel electrophoresis

Nuclear proteins were extracted from purified nuclei of 7,12-dimethylbenz(a)anthracene(DMBA)-induced tumors and normal mammary glands of the rat by enzymatic treatment. Of the 34 bands indicated by one-dimensional polyacrylamide gel electrophoresis of nuclear proteins, 6 appeared in high concentration in tumors but were found as traces or undetectable in normal glands; 6 others were clearly shown in the latter but were not detectable or greatly reduced in the former. Two-dimensional electrophoresis identified about 130 and 92 non-histone proteins in normal mammary and tumor cell nuclei respectively. Marked differences in spot density were noted especially in spots (M.W. X 10(-3)/pI) 100/5.7 and 200/5.5 of tumors and 28/7.1, 32/5.4, 36/5.4, 38/6.9, and 68/6.0 of normal tissue. The relationship between these nuclear proteins and the development of mammary tumors is also discussed.

Immunochemical and enzymatic studies on the soluble antigens of normal human kidney

The antigenic composition of the soluble extract from normal human kidney was determined with the combined techniques of immunological absorption, immuno-diffusion and immunoelectrophoresis. The kidney extract contained at least eleven non-serum, tissue antigens; some of them were found in the extracts of other organs, but three were kidney-specific. None of the soluble tissue antigens from human kidney was characterized as a lipoprotein; however, three of them stained with the reagent for glycoproteins. Esterase activities were also demonstrated in four non-serum, renal antigens, one of which was present only in the kidney extract and absent in the other organs extracts.

The properties of soluble proteins synthesized by nephrotic rat kidney microsomes

The incorporation of 14C-leucine into the microsomal proteins of nephrotic rat kidney was much higher than that in the microsomal proteins of the normal rat kidney. When the newly synthesized microsomal proteins were analyzed by acrylamide gel electrophoresis, it was found that the higher incorporation of 14C-leucine in nephrotic rat kidney was mostly due to an increase in the biosynthesis of a tissue protein which migrated in the electrophoretic zone between serum albumin and transferrin. This protein did not react with rabbit antiserum to normal rat serum and was stained with periodic acid – Schiff reagent. It was believed to be excreted in the urine of nephrotic rats in great quantity and was easily identified as a distinct band in electrophoregrams of urine from these rats.

Experimental glomerulonephritis induced with the major antigen of rat kidney

The major antigen of rat kidney (KMA) isolated in an immunochemically purified form was injected into homologous rats at 2-week intervals during 42 weeks. Circulating antibodies against KMA were constantly found in the sera of all immunized animals after 4 months of KMA treatment. Marked proteinuria accompanied by a significant increase in the serum γ-globulin level occurred only several months after the appearance of circulating antibodies. Histological examinations of the KMA-treated rat kidney revealed mild but definite glomerular lesions of the membranous, non-proliferative type. Rat <i>γ</i>-globulin was found as a mixed, linear and granular, deposit along the basement membranes and the mesangial regions. However, rat <i>β</i>_1C-globulin was found as an exclusively granular deposit in the same areas, but more intensively in the mesangium. The acid elution of KMA-treated rat kidney contained γ-globulin which reacted with KMA. As compared with Edgington’s nephritogenic tubular antigen RTE-α₅, KMA was found to be completely different. However, it was also localized exclusively in the proximal tubular cells. Its presence in normal rat serum and liver has been suggested as a source of autologous immunogens in the long-term development of an autoimmune complex nephritis in the rat.

Renal lesions associated with the Walker 256 adenocarcinoma in the rat

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Induction of experimental glomerulonephritis in the rat by homologous major urinary protein

Repeated injections of the major urinary protein (MUP) in the homologous rat produced a rise in the serum γ-globulin level, a severe proteinuria toward the end of experiment, the appearance of circulating antibodies to the major urinary protein, a hyperactivity of the lymphoid structure of the spleen and lung and particularly, renal lesions. The glomeruli showed marked thickening of the endothelial basement membrane and adhesion of the tufts with the Bowman's capsule. There were also slight alterations in the tubular basement membranes. Immunochemical studies of the experimental kidney revealed the disappearance of the kidney major antigen which was immunologically identical with the major urinary protein. The significance of the presence of circulating antibodies to major urinary protein has been discussed in relation to the biochemical and morphological changes in experimental animals. It has also been suggested that urinary proteins derived from the kidney and liver could induce glomerular lesions in the renal structure by an immunological mechanism.

Isolation and characterization of the major antigen of rat kidney

The major antigen of rat kidney (KMA) was isolated by chromatography on DEAE-cellulose and Sephadex G-25 gel filtration. The sedimentation coefficient of the purified antigen was about 1.2 S and its electrophoretic mobility corresponded to that of α2-globulins. Its diffusion coefficient was estimated by the method of Allison and Humphrey as 11.4 × 10−7 cm2sec−1. On gel filtration through Sephadex G-100, the purified preparation was resolved into two components with identical antigenic properties but of different molecular weights, estimated as 16,600 and 4,100. The concentrations of KMA were determined in different tissues, urine, and serum by immunodiffusion. The probable relationship between physical and immunochemical properties and the possible physio-pathological role of KMA are discussed.