Characterizing substructure via mixture modeling in large-scale genetic summary statistics

Genetic summary data are broadly accessible and highly useful including for risk prediction, causal inference, fine mapping, and incorporation of external controls. However, collapsing individual-level data into groups masks intra- and inter-sample heterogeneity, leading to confounding, reduced power, and bias. Ultimately, unaccounted substructure limits summary data usability, especially for understudied or admixed populations. Here, we present Summix2 , a comprehensive set of methods and software based on a computationally efficient mixture model to estimate and adjust for substructure in genetic summary data. In extensive simulations and application to public data, Summix2 characterizes finer-scale population structure, identifies ascertainment bias, and identifies potential regions of selection due to local substructure deviation. Summix2 increases the robust use of diverse publicly available summary data resulting in improved and more equitable research.

COVID-19 Mortality in the Colorado Center for Personalized Medicine Biobank

Over 6.37 million people have died from COVID-19 worldwide, but factors influencing COVID-19-related mortality remain understudied. We aimed to describe and identify risk factors for COVID-19 mortality in the Colorado Center for Personalized Medicine (CCPM) Biobank using integrated data sources, including Electronic Health Records (EHRs). We calculated cause-specific mortality and case-fatality rates for COVID-19 and common pre-existing health conditions defined by diagnostic phecodes and encounters in EHRs. We performed multivariable logistic regression analyses of the association between each pre-existing condition and COVID-19 mortality. Of the 155,859 Biobank participants enrolled as of July 2022, 20,797 had been diagnosed with COVID-19. Of 5334 Biobank participants who had died, 190 were attributed to COVID-19. The case-fatality rate was 0.91% and the COVID-19 mortality rate was 122 per 100,000 persons. The odds of dying from COVID-19 were significantly increased among older men, and those with 14 of the 61 pre-existing conditions tested, including hypertensive chronic kidney disease (OR: 10.14, 95% CI: 5.48, 19.16) and type 2 diabetes with renal manifestations (OR: 5.59, 95% CI: 3.42, 8.97). Male patients who are older and have pre-existing kidney diseases may be at higher risk for death from COVID-19 and may require special care.

COVID-19 Surveillance in the Biobank at the Colorado Center for Personalized Medicine: Observational Study

BACKGROUND

Characterizing the experience and impact of the COVID-19 pandemic among various populations remains challenging due to the limitations inherent in common data sources, such as electronic health records (EHRs) or cross-sectional surveys.

OBJECTIVE

This study aims to describe testing behaviors, symptoms, impact, vaccination status, and case ascertainment during the COVID-19 pandemic using integrated data sources.

METHODS

In summer 2020 and 2021, we surveyed participants enrolled in the Biobank at the Colorado Center for Personalized Medicine (CCPM; N=180,599) about their experience with COVID-19. The prevalence of testing, symptoms, and impacts of COVID-19 on employment, family life, and physical and mental health were calculated overall and by demographic categories. Survey respondents who reported receiving a positive COVID-19 test result were considered a "confirmed case" of COVID-19. Using EHRs, we compared COVID-19 case ascertainment and characteristics in EHRs versus the survey. Positive cases were identified in EHRs using the International Statistical Classification of Diseases, 10th revision (ICD-10) diagnosis codes, health care encounter types, and encounter primary diagnoses.

RESULTS

Of the 25,063 (13.9%) survey respondents, 10,661 (42.5%) had been tested for COVID-19, and of those, 1366 (12.8%) tested positive. Nearly half of those tested had symptoms or had been exposed to someone who was infected. Young adults (18-29 years) and Hispanics were more likely to have positive tests compared to older adults and persons of other racial/ethnic groups. Mental health (n=13,688, 54.6%) and family life (n=12,233, 48.8%) were most negatively affected by the pandemic and more so among younger groups and women; negative impacts on employment were more commonly reported among Black respondents. Of the 10,249 individuals who responded to vaccination questions from version 2 of the survey (summer 2021), 9770 (95.3%) had received the vaccine. After integration with EHR data up to the time of the survey completion, 1006 (4%) of the survey respondents had a discordant COVID-19 case status between EHRs and the survey. Using all longitudinal EHR and survey data, we identified 11,472 (6.4%) COVID-19-positive cases among Biobank participants. In comparison to COVID-19 cases identified through the survey, EHR-identified cases were younger and more likely to be Hispanic.

CONCLUSIONS

We found that the COVID-19 pandemic has had far-reaching and varying effects among our Biobank participants. Integrated data assets, such as the Biobank at the CCPM, are key resources for population health monitoring in response to public health emergencies, such as the COVID-19 pandemic.

Summix: A method for detecting and adjusting for population structure in genetic summary data

Publicly available genetic summary data have high utility in research and the clinic, including prioritizing putative causal variants, polygenic scoring, and leveraging common controls. However, summarizing individual-level data can mask population structure, resulting in confounding, reduced power, and incorrect prioritization of putative causal variants. This limits the utility of publicly available data, especially for understudied or admixed populations where additional research and resources are most needed. Although several methods exist to estimate ancestry in individual-level data, methods to estimate ancestry proportions in summary data are lacking. Here, we present Summix, a method to efficiently deconvolute ancestry and provide ancestry-adjusted allele frequencies (AFs) from summary data. Using continental reference ancestry, African (AFR), non-Finnish European (EUR), East Asian (EAS), Indigenous American (IAM), South Asian (SAS), we obtain accurate and precise estimates (within 0.1%) for all simulation scenarios. We apply Summix to gnomAD v.2.1 exome and genome groups and subgroups, finding heterogeneous continental ancestry for several groups, including African/African American (∼84% AFR, ∼14% EUR) and American/Latinx (∼4% AFR, ∼5% EAS, ∼43% EUR, ∼46% IAM). Compared to the unadjusted gnomAD AFs, Summix's ancestry-adjusted AFs more closely match respective African and Latinx reference samples. Even on modern, dense panels of summary statistics, Summix yields results in seconds, allowing for estimation of confidence intervals via block bootstrap. Given an accompanying R package, Summix increases the utility and equity of public genetic resources, empowering novel research opportunities.

Abstract 4615: Admixture mapping and gene expression analysis to identify candidate genes associated with HER2 positive breast cancer in Latinas

The incidence of Human Epidermal Growth Factor Receptor 2 positive (HER2+) breast cancer is higher in Latinas, both in the U.S. and in Latin America. Preliminary analyses of the Peruvian Genetics and Genomics of Breast Cancer (PEGEN-BC) study data set showed a strong association between the Indigenous American (IA) component of ancestry and HER2 status independently of stage at diagnosis and other factors. The aim of this study was to identify genetic loci associated with genetic ancestry and HER2+ breast cancer in patients with high IA ancestry. To achieve this aim we used admixture mapping and gene-expression guided fine mapping.

Breast cancer patients were recruited at the Instituto Nacional de Enfermedades Neoplásicas in Lima, Peru. A total of 1,850 patients have been recruited to date. DNA samples are currently available for a total of 1,380 patients. Genome wide genotypes were obtained with the Affymetrix Precision Medicine Research Array. After quality control, genome wide genotype data was available for 1,312 patients. After LD pruning and exclusion of SNPs with minor allele frequency <0.05, we estimated global ancestry with the program ADMIXTURE and locus-specific ancestry using RFMix. Tumor subtypes were classified using immunohistochemistry markers for estrogen, progesterone and HER2 receptors. Admixture mapping was conducted using logistic regression models. The outcome variable was HER2 status (HER2+ =1, HER2- =0). Global Individual IA ancestry and age at diagnosis were included as covariates. For transcriptomic analysis within regions of interest we used exome sequencing data (Illumina NextSeq500 system) for total RNA extracted from 79 FFPE tumor tissues from the same cohort. Genes within regions with suggestive admixture mapping signals were further analyzed by comparing normalized RNA read counts by HER2+ status using the DEseq2 R package.

Admixture mapping analysis revealed two regions associated with IA ancestry in two chromosomal regions: 2q11-2q12 (OR=0.6, p=0.00009) and 3p14 (OR=1.5, p= 0.0004). Of the 44 genes within the 2q region, TGFBRAP1, member of the heat shock protein 90 family, was the only gene with suggestive differential expression by HER2 status (p=0.032). Of the 28 genes within the 3p14 region, we found significant differential expression for FLNB (lower expression in HER2+ tumours, 5%FDR= 0.03), which has been shown to supress tumour growth and metastasis.

Combining admixture mapping and transcriptomics is a promising approach to discover candidate genes associated with subtype-specific breast cancer risk. We are currently working to replicate suggestive findings and expand our sample size to increase power.

Citation Format: Valentina Zavala, Katie M. Marker, Tatiana Vidaurre, Jeannie Navarro-Vasquez, Sandro Casavilca, Mónica Calderon, Julio Abugattas, Henry Gómez, Hugo Fuentes, Ruddy Liendo-Picoaga, Jose M. Cotrina, Silvia P. Neciosup, Carlos A. Castaneda, Zaida Morante, Fernando Valencia, Silvia J. Serrano-Gomez, Jovanny Zabaleta, Laura Fejerman. Admixture mapping and gene expression analysis to identify candidate genes associated with HER2 positive breast cancer in Latinas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4615.

Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer Is Associated with Indigenous American Ancestry in Latin American Women

Women of Latin American origin in the United States are more likely to be diagnosed with advanced breast cancer and have a higher risk of mortality than non-Hispanic White women. Studies in U.S. Latinas and Latin American women have reported a high incidence of HER2 positive (+) tumors; however, the factors contributing to this observation are unknown. Genome-wide genotype data for 1,312 patients from the Peruvian Genetics and Genomics of Breast Cancer Study (PEGEN-BC) were used to estimate genetic ancestry. We tested the association between HER2 status and genetic ancestry using logistic and multinomial logistic regression models. Findings were replicated in 616 samples from Mexico and Colombia. Average Indigenous American (IA) ancestry differed by subtype. In multivariate models, the odds of having an HER2+ tumor increased by a factor of 1.20 with every 10% increase in IA ancestry proportion (95% CI, 1.07-1.35; P = 0.001). The association between HER2 status and IA ancestry was independently replicated in samples from Mexico and Colombia. Results suggest that the high prevalence of HER2+ tumors in Latinas could be due in part to the presence of population-specific genetic variant(s) affecting HER2 expression in breast cancer. SIGNIFICANCE: The positive association between Indigenous American genetic ancestry and HER2+ breast cancer suggests that the high incidence of HER2+ subtypes in Latinas might be due to population and subtype-specific genetic risk variants.

Abstract 1589: Breast cancer subtype GWAS in Peruvian breast cancer patients

Background: We previously investigated genetic ancestry associations with breast cancer subtypes in Peruvian women. We found that women with human epidermal growth factor receptor 2 (HER2) over-expressing tumors had higher Indigenous American ancestry than women with other subtypes. We found a suggestive association between African ancestry and triple negative breast cancer (TNBC). We hypothesized that these associations could be due to the presence of germline variants in the Indigenous American genome or the African genome predisposing women to HER2 over-expression or TNBC respectively. We conducted genome wide association analyses to explore this hypothesis.

Methods: Blood samples and clinical data were collected from 1195 women with breast cancer at the Instituto Nacional de Enfermedades Neoplasicas in Lima, Peru. Genotypic profiles for 821 women were generated using the Affymetrix Precision Medicine Research Array. Four major breast cancer subtypes were identified using immunohistochemical markers (luminal A, luminal B, triple negative, and HER2 over-expressing). Genetic ancestry was determined using ADMIXTURE. Genome wide association analyses were conducted in PLINK.

Results: Three polymorphisms with the lowest p values in the TNBC GWAS are of interest. A variant, rs16910137, at 10q26, is located in an intron of the Glutaredoxin 3 gene (GLRX3 or TXNL2, OR = 2.45, P = 8.60*10-07). The protein encoded by this gene may inhibit apoptosis and play a role in cellular growth. It has also been described as a biomarker for TNBC. Our own RNA-seq data for TXNL2 in 52 Colombian women with breast cancer showed that the expression level of this gene is higher in women with triple negative (N=9) compared to luminal tumors (N=43) (P=0.06). The other two variants, rs12327440 and rs13381183, are located in an intron of the Mitogen-Activated Protein Kinase 4 (MAPK4) gene at 18q21 (OR = 0.44 and 1.94 respectively, P = 4.92*10-07 and 7.230*10-06). RNA-seq data for MAPK4 suggestively showed that the expression level is higher in women with TNBC compared to luminal tumors (P=0.18). The variant in the HER2 over-expressing GWAS with the lowest p value, rs11594103, at 10p11 is located upstream of the Enhancer Of Polycomb Homolog 1 (EPC1) gene (OR = 2.38, P = 8.03*10-07). The encoded protein has been linked to apoptosis and DNA repair among other functions and suggested as involved in the activation of metastasis.

Conclusions: Our data suggests that a germline variant within the GLRX3/TXNL2 gene might be associated with the risk of developing TNBC compared to other subtypes. This is particularly interesting in the light that previous work suggested that TXNL2 autoantibodies could be biomarker of TNBC. The MAPK4 and EPC1 genes have been previously implicated in multiple types of cancer and our results indicate that they may play a role in the etiology of specific breast cancer subtypes. This supports the importance of conducting genetic association studies in diverse samples.

Citation Format: Katie M. Marker, Tatiana Vidaurre, Jeannie Navarro Vasquez, Valentina Zavala, Silvia Serrano Gomez, Lizeth Tamayo, Renzo Meza Florez, S Casavilca, M Calderon, JE Abugattas, Henry Gómez, Hugo Fuentes, CL Monge Pimentel, Sikai Song, Daniel Cherry, Scott Huntsman, Donglei Hu, Elad Ziv, Laura Fejerman. Breast cancer subtype GWAS in Peruvian breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1589.

A truncated precursor form of prostate-specific antigen is a more specific serum marker of prostate cancer

Prostate-specific antigen (PSA) is a widely used serum marker for prostate cancer (PCa) but has limited specificity for distinguishing early PCa from benign prostatic hyperplasia, because both PCa and benign prostatic hyperplasia release PSA into the serum. We have identified previously a truncated form of precursor PSA (pPSA) in prostate tumor extracts consisting of PSA with a serine-arginine pro leader peptide ([-2]pPSA) instead of the normally expressed 7 amino acid pro leader peptide. In the current study we developed monoclonal antibodies to detect [-2]pPSA and other isoforms of pPSA for Western blot analysis. PSA was immunoaffinity purified from 100 to 200 ml of serum from each of five men with biopsy-proven cancer and three biopsy-negative men, all with total PSA levels in the diagnostically relevant range near 10 ng/ml. The truncated [-2]pPSA was estimated to range from 25 to 95% of the free PSA in the five PCa samples but only 6-19% of the free PSA in the biopsy-negative men. Immunohistochemical studies showed positive staining for [-2]pPSA in PCa epithelium and that [-2]pPSA was enriched in cancer cell secretions. In vitro activation studies showed that human kallikrein 2 and trypsin readily activated full-length pPSA but were unable to activate [-2]pPSA to mature PSA. Thus, [-2]pPSA, once formed, is a stable but inactive isoform of PSA. Truncated [-2]pPSA may represent an important new diagnostic marker for the early detection of PCa.

Seminal plasma contains "BPSA," a molecular form of prostate-specific antigen that is associated with benign prostatic hyperplasia

BACKGROUND

We previously reported that levels of BPSA, a modified form of prostate-specific antigen (PSA), are significantly elevated in prostate transition-zone tissue exhibiting nodular hyperplastic changes associated with the presence of benign prostatic hyperplasia (BPH). BPSA was purified and found to contain a characteristic clip between Lys182 and Ser183. We now describe the identification of BPSA in seminal plasma.

METHODS

PSA was purified from seminal plasma by immunoaffinity chromatography. The purified PSA was further resolved by hydrophobic interaction chromatography, and the individual PSA forms were analyzed by gel electrophoresis and N-terminal amino-acid sequencing.

RESULTS

BPSA comprised about 8% of the PSA in pooled seminal plasma, and was identical to BPSA purified from prostate tissues. BPSA was cleanly resolved from all active and inactive forms of PSA. Other inactive forms of PSA in seminal plasma consisted largely of PSA clipped at Lys145, though about 30% of the inactive seminal plasma PSA was intact, mature PSA.

CONCLUSIONS

BPSA represents a distinct form of inactive PSA in the seminal plasma that may represent a specific marker for the biochemical changes associated with nodular development in the prostate transition zone found in patients with BPH.

A dual-monoclonal sandwich assay for prostate-specific membrane antigen: levels in tissues, seminal fluid and urine

BACKGROUND

Prostate-specific membrane antigen (PSMA) is a 750-residue integral membrane glycoprotein and the target of an in-vivo imaging agent for metastatic prostate carcinoma (PCa). PSMA expression in normal and diseased prostatic tissues has previously been demonstrated by immunohistochemical techniques. In order to quantify PSMA levels in tissue homogenates and physiological fluids, we have developed a dual monoclonal antibody (mAb) sandwich assay which detects the antigen at a sensitivity <1 ng/mL and which is linear across the working range 0-50 ng/mL.

METHODS

The assay involves capture of the PSMA by a biotinylated mAb (7E11) immobilized onto a streptavidin-coated microtiter plate; this mAb binds to the N-terminus of the antigen. The captured PSMA is detected by an Eu-labelled mAb (PEQ226) which binds in the region corresponding to Residues 134-437 of the antigen. PSMA was purified from LNCaP cells by immunoaffinity chromatography, and used as a calibrator, based on its concentration by the bicinchoninic acid (BCA) protein assay.

RESULTS

The assay was applied to a panel of normal and tumor tissues. Levels were highest in the prostate tissues (292-4254 ng/mg protein). Low levels (21-51 ng/mL) were observed in membranes from ovary and breast, and neglible levels (1-10 ng/mg) in membranes from skin, liver, intestine, and kidney. Levels in the corresponding cytosol fractions were 20-to 50-fold lower. The average PSMA level in seminal fluid from 21 donors was 9, 012 ng/mL. On average, levels in normal-male urine (3.47 ng/mL) were ten-fold higher than in normal-female urine (0.3 ng/mL).

CONCLUSIONS

This report is the first to describe absolute quantitation of PSMA in tissues and fluids. Congruent with earlier tissue studies based on immunohistochemical staining and Western-blot analysis, prostate tissue membranes expressed the highest levels of PSMA.

Identification of a novel complex between human kallikrein 2 and protease inhibitor-6 in prostate cancer tissue

Human kallikrein (hK) 2 is an arginine-selective serine protease expressed predominantly in the prostate that has an 80% sequence identity with prostate-specific antigen. Expression of hK2 is elevated in the tumor epithelium compared to benign prostate tissue. We have purified, sequenced, and identified a novel hK2 complex in prostate tissue consisting of hK2 and a serine protease inhibitor known as protease inhibitor-6 (PI-6). This 64-kDa SDS-PAGE stable complex is elevated in the tumor and is approximately 10% of total hK2. No comparable complex of prostate-specific antigen was detected. PI-6, also known as cytoplasmic antiprotease, has been characterized as an intracellular inhibitor of trypsin and chymotrypsin-like proteases, which has high homology to plasminogen activator inhibitor 1 and 2. The physiological role of PI-6 in the prostate and its relationship to hK2 and prostate cancer are under investigation.

Ala217 is important for the catalytic function and autoactivation of prostate-specific human kallikrein 2

Prostate-specific human kallikrein, hK2, is a serine protease found in prostate tissues that has 78% amino acid sequence identity with prostate-specific antigen (PSA). We have previously reported the affinity purification of hK2 heterologously expressed in a hamster cell line and demonstrated an arginine-restricted substrate specificity. Here, we describe the cloning, expression, purification, and enzymatic activity of a mutant form of hK2 containing an alanine to valine substitution at residue 217 ([Val217]hK2). This mutant form was secreted into the serum-free spent media of recombinant cells as the stable proenzyme form ([Val217]phK2). Mild trypsin treatment was used to convert [Val217]phK2 to the active form, which had reduced catalytic function compared to the wild-type hK2. Kinetic studies using the chromogenic substrate D-H-Pro-Phe-Arg-4-nitroanilide showed that [Val217]hK2 has significantly decreased substrate binding, with a K(m) of 4200 microM compared to 11 microM for wild-type hK2. The k(cat) for [Val217]hK2 was more than 100-fold lower than for hK2. hK2, but not [Val217]hK2, was able to activate [Val217]phK2. [Val217]hK2 also showed altered specificity on a synthetic peptide substrate compared to wild-type hK2, which exhibited partial hydrolysis at a PSA chymotrypsin-like cleavage site as well as the trypsin-like site cleaved by hK2. These results indicate that Ala217 is a key residue affecting the catalytic properties of hK2.