Population Genetic Screening Research Articles

9227 Haptoglobin-related protein (HPR) new role as insulin secretion enhancer

Abstract Disclosure: Carlos Viesi, Ph.D.[1], Ian Tamburini, BS[1], Hosung Bae, Ph.D[1]., Erwin Ilegems, Ph.D.[2], Leandro Velez, Ph.D. [1], Mingqi Zhou, BS[1], Christy Nguyen, Ph.D.[1], Casey Johnson, Ph.D.[1], Cholsoon Jang, Ph.D[1]., Erika Nishimura[2] and Marcus Seldin, Ph.D.[1]. [1]Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, USA, [2]Departments of Diabetes Protein Engineering, Diabetes Biology & Pharmacology, Medicinal Chemistry, Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark. Type 2 Diabetes (T2D) affects over 530 million people around the globe. Insulin resistance, encompassing tissues such as muscle, adipose, and liver, is the initial step hallmarked by hyperinsulinemia. Coupled with β-cell failure, these coordinated responses progress to T2D, becoming irreversible and medically challenging. Despite the well-established requirement for communication between pancreas and peripheral tissues in T2D progression, this area remains almost entirely unexplored. Here, we performed a human population genetic screening across 310 individuals to search for new endocrine regulators of pancreas function. Specifically, global gene expression from 18 peripheral tissues was analyzed to identify potential endocrine regulators of insulin secretion. This analysis prioritized liver-specific Haptoglobin-related protein (HPR) as genetically-enriched with islet insulin responses. Mouse models using AAV technology and acute protein administration of HPR showed that this newly secreted protein is sufficient to prevent diet-induced insulin resistance through enhanced beta-cell respiration. When mice were administered soluble HPR, then pancreatic tissue subjected to global RNA-sequencing, enhanced respiration pathways were observed. Next, we generated hepatocyte-specific overexpression models using AAV, which were sufficient to rescue whole-body glucose disposal profiles and weight gain in diet-induced insulin-resistant mice. Altogether, these findings highlight HPR as a novel soluble protein which signals from liver to pancreatic islets. Presentation: 6/3/2024

8258 Haptoglobin-related protein (HPR) new role as insulin secretion enhancer

Abstract Disclosure: C. Viesi: None. Type 2 Diabetes (T2D) affects over 530 million people around the globe. Insulin resistance, encompassing tissues such as muscle, adipose, and liver, is the initial step hallmarked by hyperinsulinemia. Coupled with β-cell failure, these coordinated responses progress to T2D, becoming irreversible and medically challenging. Despite the well-established requirement for communication between pancreas and peripheral tissues in T2D progression, this area remains almost entirely unexplored. Here, we performed a human population genetic screening across 310 individuals to search for new endocrine regulators of pancreas function. Specifically, global gene expression from 18 peripheral tissues was analyzed to identify potential endocrine regulators of insulin secretion. This analysis prioritized liver-specific Haptoglobin-related protein (HPR) as genetically-enriched with islet insulin responses. Mouse models using AAV technology and acute protein administration of HPR showed that this newly secreted protein is sufficient to prevent diet-induced insulin resistance through enhanced beta-cell respiration. When mice were administered soluble HPR, then pancreatic tissue subjected to global RNA-sequencing, enhanced respiration pathways were observed. Next, we generated hepatocyte-specific overexpression models using AAV, which were sufficient to rescue whole-body glucose disposal profiles and weight gain in diet-induced insulin-resistant mice. Altogether, these findings highlight HPR as a novel soluble protein which signals from liver to pancreatic islets. Presentation: 6/3/2024

Population Screening for Hereditary Haemochromatosis-Should It Be Carried Out, and If So, How?

The Human Genome Project, completed in 2003, heralded a new era in precision medicine. Somewhat tempering the excitement of the elucidation of the human genome is the emerging recognition that there are fewer single gene disorders than first anticipated, with most diseases predicted to be polygenic or at least gene-environment modified. Hereditary haemochromatosis (HH) is an inherited iron overload disorder, for which the vast majority of affected individuals (>90%) have homozygosity for a single pathogenic variant in the HFE gene, resulting in p.Cys282Tyr. Further, there is significant benefit to an individual in identifying the genetic risk of HH, since the condition evolves over decades, and the opportunity to intervene and prevent disease is both simple and highly effective through regular venesection. Add to that the immediate benefit to society of an increased pool of ready blood donors (blood obtained from HH venesections can generally be used for donation), and the case for population screening to identify those genetically at risk for HH becomes more cogent. Concerns about genetic discrimination, creating a cohort of "worried well", antipathy to acting on medical advice to undertake preventive venesection or simply not understanding the genetic risk of the condition adequately have all been allayed by a number of investigations. So why then has HH population genetic screening not been routinely implemented anywhere in the world? The answer is complex, but in this article we explore the pros and cons of screening for HH and the different views regarding whether it should be phenotypic (screening for iron overload by serum ferritin and/or transferrin saturation) or genotypic (testing for HFE p.Cys282Tyr). We argue that now is the time to give this poster child for population genetic screening the due consideration required to benefit the millions of individuals at risk of HFE-related iron overload.

An improved and effective DNA extraction protocol for Pyracantha crenulata with optimal PCR reliability

Abstract There are many challenges involved in obtaining high-quality DNA from tissues/cells, especially when using plants as the raw material. Three different DNA extraction protocols were employed in order to isolate high quality of genomic DNA from Pyracantha crenulata leaves. P. crenulata is a complex, versatile, and evergreen shrub species in Rosaceae family which is ecologically, economically and culturally important. This species produces valuable antioxidants like polyphenols, polysaccharides and secondary metabolites which interfere with DNA extraction thus making molecular marker based studies difficult in this species. This study aimed to develop a simple, rapid, cost-effective and highly efficient protocol for P. crenulata leaves rich in salts and phenols. The results demonstrated that modified CTAB (double buffer) protocol is very effective in overcoming the challenges that could impede next-generation sequencing analysis. The yield of the extracted DNA was excellent ranging from 368 to 410 ng/μL DNA with A260/280 ratio ranging from 1.80 to 1.84. The extracted DNA was amenable to PCR amplification making it suitable for DNA-based molecular marker studies. None procedures have been published for the purpose up this species, therefore, double buffer based extraction protocol is reported for the first time in P. crenulata and might prove useful in other species of family Rosa-ceae. This study describes an effective DNA isolation method that is appropriate for frequent population genetic screening. In conclusion, the double buffer protocol showed the most efficient and effective approach for extracting DNA from phenol rich, fresh, mature, and dry leaves.

The new face of cystic fibrosis in the era of population genetic carrier screening

BackgroundPopulation genetic carrier screening (PGCS) for cystic fibrosis (CF) has been offered to couples in Israel since 1999 and was included in a fully subsidized national program in 2008. We evaluated the impact of PGCS on CF incidence, genetic and clinical features. MethodsThis was a retrospective national study. Demographic and clinical characteristics of children with CF born in Israel between 2008 and 2018 were obtained from the national CF registry and from patients' medical records. Data on CF births, preimplantation genetic testing (PGT), pregnancy termination and de-identified data from the PGCS program were collected. ResultsCF births per 100,000 live births decreased from 8.29 in 2008 to 0.54 in 2018 (IRR = 0.84, p < 0.001). The CF pregnancy termination rate did not change (IRR = 1, p= 0.9) while the CF-related PGT rate increased markedly (IRR = 1.33, p < 0.001). One hundred and two children were born with CF between 2008 and 2018 with a median age at diagnosis of 4.8 months, range 0–111 months. Unlike the generally high uptake nationally, 65/102 had not performed PGCS. Even if all had utilized PGCS, only 51 would have been detected by the existing genetic screening panel. Clinically, 34 % of children were pancreatic sufficient compared to 23 % before 2008 (p = 0.04). ConclusionsSince institution of a nationwide PGCS program, the birth of children with CF decreased markedly. Residual function variants and pancreatic sufficiency were more common. A broader genetic screening panel and increased PGCS utilization may further decrease the birth of children with CF.

Risk perception and intended behavior change after uninformative genetic results for adult-onset hereditary conditions in unselected patients.

Population genetic screening for preventable adult-onset hereditary conditions may improve disease management and morbidity but most individuals will receive uninformative results that do not indicate higher risk for disease. Investigation into subsequent psychosocial health and behaviors is necessary to inform population screening feasibility, effectiveness, and cost considerations. We conducted a prospective survey study of unselected University of Washington Medicine patients enrolled in a genetic research study screening for pathogenic variation in medically important genes. Survey questions adapted from the Feelings About genomiC Testing Results (FACToR) questionnaire and designed to understand perceived disease risk change and planned health behaviors were administered after receipt of results. Overall, 2761 people received uninformative results and 1352 (49%) completed survey items. Respondents averaged 41 years old, 62% were female, and 56% were Non-Hispanic Asian. Results from the FACToR instrument showed mean (SD) scores of 0.92 (1.34), 7.63 (3.95), 1.65 (2.23), and 0.77 (1.50) for negative emotions, positive emotions, uncertainty, and privacy concerns, respectively, suggesting minimal psychosocial harms from genetic screening. Overall, 12.2% and 9.6% of survey respondents believed that their risk of cancer or heart disease, respectively, had changed after receiving their uninformative genetic screening results. Further, 8.5% of respondents planned to make healthcare changes and 9.1% other behavior changes. Future work is needed to assess observed behavior changes attributable to uninformative screening results and if small changes in behavior among this population have large downstream impacts.

Diagnostic yield of genetic screening in a diverse, community-ascertained cohort

BackgroundPopulation screening for genetic risk of adult-onset preventable conditions has been proposed as an attractive public health intervention. Screening unselected individuals can identify many individuals who will not be identified through current genetic testing guidelines.MethodsWe sought to evaluate enrollment in and diagnostic yield of population genetic screening in a resource-limited setting among a diverse population. We developed a low-cost, short-read next-generation sequencing panel of 25 genes that had 98.4% sensitivity and 99.98% specificity compared to diagnostic panels. We used email invitations to recruit a diverse cohort of patients in the University of Washington Medical Center system unselected for personal or family history of hereditary disease. Participants were sent a saliva collection kit in the mail with instructions on kit use and return. Results were returned using a secure online portal. Enrollment and diagnostic yield were assessed overall and across race and ethnicity groups.ResultsOverall, 40,857 people were invited and 2889 (7.1%) enrolled. Enrollment varied across race and ethnicity groups, with the lowest enrollment among African American individuals (3.3%) and the highest among Multiracial or Other Race individuals (13.0%). Of 2864 enrollees who received screening results, 106 actionable variants were identified in 103 individuals (3.6%). Of those who screened positive, 30.1% already knew about their results from prior genetic testing. The diagnostic yield was 74 new, actionable genetic findings (2.6%). The addition of more recently identified cancer risk genes increased the diagnostic yield of screening.ConclusionsPopulation screening can identify additional individuals that could benefit from prevention, but challenges in recruitment and sample collection will reduce actual enrollment and yield. These challenges should not be overlooked in intervention planning or in cost and benefit analysis.

Precision medicine in Australia: now is the time to get it right.

Precision medicine in Australia: now is the time to get it right.

Assessing Vietnamese American patient perspectives on population genetic testing in primary care: A community-engaged approach.

SummaryAchieving health equity in precision medicine remains a critical challenge because of the continued underrepresentation of non-white populations in research and barriers to genetic services. The goal of this study was to explore Vietnamese American (VA) participant views toward incorporating genetics in routine healthcare to better serve the local VA community within an integrated health system offering primary care-based population genetic testing to adults for conditions that could be prevented or mitigated when detected early. We conducted semi-structured interviews from August–September 2021, with 22 individuals receiving primary care who self-identified as Vietnamese or VA, and employed rapid qualitative analysis (RQA) to identify key concepts. Community research team members participated in study design, data collection, RQA, and reporting. Findings from the interviews revealed that several participant perceived challenges to genetic testing, which included lack of information, fear of results impact, cost, and privacy concerns. Participants suggested various ways to overcome some of these barriers, such as decreasing the cost of testing, receiving information from a trusted physician, using preferred education strategies in the community, and having convenient access to testing. Study participants also shared a variety of trusted sources they would seek out for advice on genetic testing. This study with VAs identified barriers, facilitators, and messengers to offering genetic testing in a local healthcare context and demonstrated how community-engaged research coupled with RQA is a promising approach for healthcare institutions as they identify needs and tailor strategies for implementing population genetic screening programs in local ethnic communities.

Public Interest in Population Genetic Screening for Cancer Risk.

An emerging role for DNA sequencing is to identify people at risk for an inherited cancer syndrome in order to prevent or ameliorate the manifestation of symptoms. Two cancer syndromes, Hereditary Breast and Ovarian Cancer and Lynch Syndrome meet the “Tier 1” evidence threshold established by the Centers for Disease Control and Prevention (CDC) for routine testing of patients with a personal or family history of cancer. Advancements in genomic medicine have accelerated public health pilot programs for these highly medically actionable conditions. In this brief report, we provide descriptive statistics from a survey of 746 US respondents from a Qualtrics panel about the public’s awareness of genetic testing, interest in learning about their cancer risk, and likelihood of participating in a population genetic screening (PGS) test. Approximately of half the respondents were aware of genetic testing for inherited cancer risk (n = 377/745, 50.6%) and would choose to learn about their cancer risk (n-309/635, 48.7%). Characteristics of those interested in learning about their cancer risk differed by educational attainment, age, income, insurance status, having a primary care doctor, being aware of genetic testing, and likelihood of sharing information with family (p < 0.05). A sizeable majority of the respondents who were interested in about learning their cancer risk also said that they were likely to participate in a PGS test that involved a clinical appointment and blood draw, but no out-of-pocket cost (n = 255/309, 82.5%). Reasons for not wanting to participate included not finding test results interesting or important, concerns about costs, and feeling afraid to know the results. Overall, our results suggest that engaging and educating the general population about the benefits of learning about an inherited cancer predisposition may be an important strategy to address recruitment barriers to PGS.

P793: SCREENING OF NATURALLY OCCURRING CXCR4 VARIANTS FOR IDENTIFICATION OF NOVEL PATHOGENIC MUTATIONS FOR WHIM SYNDROME

Background: WHIM (Warts, Hypogammaglobulinemia, Infections, Myelokathexis) syndrome is a rare, autosomal-dominant primary immunodeficiency marked by neutropenia and lymphopenia. Classically, WHIM syndrome pathogenesis is causally linked to a variety of heterozygous gain-of-function mutations in the C-terminus of chemokine receptor CXCR4, a master regulator of immune cell trafficking and homeostasis. As of February 2022, 18 variants in CXCR4 have been implicated in WHIM syndrome, while a substantial number remain unexplored for their association with the disease. Using in vitro functional assays, we previously found that impaired receptor internalization and enhanced chemotaxis are conserved in all CXCR4WHIM variants and that defective internalization correlates with neutropenia, the most penetrant phenotype of patients with WHIM syndrome. We used this approach to confirm functional defects in primary cells isolated from patients harboring a novel variant, suggesting that the in vitro profiling approach can potentially drive identification of pathogenic variants. Aims: We aimed to functionally characterize multiple previously uncharacterized variants of CXCR4 using in vitro assays. We also examined allele frequencies of these novel variants to estimate the potential number of individuals harboring these variants with a long-term goal of determining the actual prevalence of WHIM syndrome. Methods: The CXCR4-negative K562 cell line was used as a model system to express 53 novel CXCR4 variants identified in patient and population databases (ClinVar, Ensembl, CentoMD, GnomAD) and genetic screening initiatives (Invitae PATH4WARD) found in the C-terminus (hotspot of CXCR4WHIM mutations) as well as throughout the protein. The effects of these mutations on CXCR4 internalization and chemotaxis were studied in cells stimulated with the C-X-C chemokine ligand 12 (CXCL12). The in vitro functional parameters were compared with known pathogenic CXCR4 variants and were used to assign a cumulative score (impaired internalization + enhanced chemotaxis) of functional defect severity. Results: Out of 53 selected variants, 42 were missense (ms), 6 were frameshift (fs), 3 were nonsense (ns), and 2 were transcript variants (tv). Eighteen of the screened variants led to a decreased internalization of CXCR4 in comparison to the wild-type (WT) receptor upon stimulation with CXCL12 while 20 variants demonstrated enhanced chemotaxis of cells toward CXCL12. Overall, 34 variants showed defects in at least one CXCR4-dependent marker. Correlation analysis and scoring of the functional parameters in cells expressing mutated or CXCR4WT revealed 17 variants (9 ms, 5 fs, 2 ns, 1 tv) that co-segregated with the known pathogenic WHIM variants. Finally, white blood cell counts in 3 patients harboring novel variants showed that CXCR4 internalization defects in vitro correlated with the severity of neutropenia. Summary/Conclusion: This is the first study characterizing functional impairments in naturally occurring CXCR4 variants via a pipeline of assays intended to predict pathogenicity. Seventeen CXCR4 variants were identified (several outside the C-terminus of CXCR4) that caused in vitro functional defects resembling those exhibited by known WHIM variants. Many (10/17) of these newly identified variants are present at high frequencies (4.4 × 10-4–8.0 × 10-6) in genomic databases. Potential association of these variants with WHIM syndrome is under investigation and is likely to expand current estimates of WHIM syndrome prevalence.

A new lizard species (Scincidae: Ctenotus) highlights persistent knowledge gaps on the biodiversity of Australia’s central deserts

Australia harbors the most diverse lizard assemblages on Earth, yet the biodiversity of its vast arid zone remains incompletely characterized. Recent sampling of remote regions has revealed new species with unique phenotypes and unclear evolutionary affinities. Here, we describe a new species of scincid lizard that appears to be widely distributed across the Great Victoria Desert and adjacent regions. The new species was previously overlooked among specimens of the wide-ranging desert taxon Ctenotus schomburgkii but is distinguished from it by coloration and scalation characters. Phylogenetic analyses based on mitochondrial and genome-wide nuclear loci confirmed that the new species is highly divergent from C. schomburgkii, with which it appears to be sympatric across much of its range. In addition to the new species, our survey of genetic variation within C. schomburgkii as currently recognized revealed three additional lineages that approach one another in southern and northwestern Australia, and which may also represent distinct species. These results suggest that our knowledge of the extraordinary biodiversity of arid Australia remains incomplete, with implications for the conservation and management of this unique fauna. The targeted collection of voucher specimens in undersampled regions, coupled with population genetic screening of lineage diversity, will be crucial for characterizing species boundaries and understanding the composition of Australia’s vertebrate communities.

EP493: Population genetic screening study participants intend to share test results with family members

Multiple research projects are currently undertaking large-scale studies to screen for a variety of preventable genetic diseases at the population level. To maximize the effect of population genetic screening, testing results should be shared with family members who may also be impacted by these results. Prior studies have shown high rates of results sharing after clinical genetic testing, but significantly lower rates of sharing of results from direct-to-consumer testing. It is unknown if those electing to undergo genetic screening as part of a population cohort will have the same information sharing patterns as those referred for clinical genetic testing based on family or personal history.

EP072: Disparities of racial and ethnic minorities in population genetic screening: Evidence and promising strategies

Epidemiological data suggested inequitable access to healthcare services to patients of racial and ethnic minorities in comparison to other predominant populations. Consanguinity is common among ethnic minorities and medical conditions, carrier frequency, and the founder variants are relatively unknown. The aim is to improve healthcare access, delivery, and population genetic screening for these populations, advocate for primary prevention, minimize the psychological and economical burden and assess the application of expanded carrier testing.

EP476: Applying implementation science to support the success of a precision health initiative in a learning health system

Genetic information is increasingly relevant for disease prevention and risk management at the individual and population levels. Rapidly decreasing sequencing cost and increased throughput ability have paved the way for population-level genetic and genomic testing to support precision medicine and population health. Despite the accessibility of genetic information, challenges exist to scaling up these approaches, including engaging large multidisciplinary teams of researchers and clinicians, ensuring public understanding of genetic information, equitable access and participation in genetic screening, and sustainability of population genetic screening programs.

Long‐term translocation explains population genetic structure of a recreationally fished iconic species in Japan: Combining current knowledge with reanalysis

AbstractAyu (Plecoglossus altivelis altivelis) is an important freshwater fisheries resource and popular recreational fishing species in Japan that lives for only 1 year, with a single breeding season. To supplement increased recreational fishing demand for this species, more than 13 million wild‐born landlocked juveniles are translocated every year from Lake Biwa into Japanese rivers, and more than 52 million hatchery‐reared juveniles born from captive‐reared parents have been extensively released. The translocation of landlocked juveniles and hatchery release has continued for more than 100 and 30 generations, respectively. Previous studies have reported that landlocked and amphidromous forms of Ayu easily hybridise, leading to concerns that the fitness of hybrid progeny would be reduced in the wild. However, limited information exists regarding the reproductive success of landlocked Ayu in translocated rivers, and to date no studies have evaluated the effects of translocation on population structure. Demonstrating that hybridisation occurs between the two forms is central to future management and conservation of this species. To address this, a literature search to summarise biological knowledge of Ayu and population genetic data screening was undertaken, and published genetic data sets covering a distribution range in Japan were reanalysed. Analyses provide strong evidence for very high gene flow between sampling locations. Genetic diversity is homogeneous in amphidromous samples. Bayesian admixture analysis infers widespread hybridisation in Japanese rivers (24 ± 8%). Maximum likelihood admixture graphs detect two migration events from Lake Biwa to rivers in the northern Sea of Japan and Hokkaido. Analyses consistently indicate that hybridisation between translocated landlocked juveniles and native amphidromous Ayu occurs throughout Japanese rivers. These results are discussed in relation to the management of this species.

Barriers and Facilitators for Population Genetic Screening in Healthy Populations: A Systematic Review

Barriers and Facilitators for Population Genetic Screening in Healthy Populations: A Systematic Review

Public Interest in Population Genetic Screening for Cancer Risk

Public Interest in Population Genetic Screening for Cancer Risk

Re-Evaluating Race Adjustment in Prenatal AFP Screening

The association of maternal serum alpha fetoprotein (AFP) levels and neural tube defects (NTD) was reported over 50 years ago. Risk adjustment for race is commonly used in interpreting AFP. Modern appraisal of race as a social construct necessitates re-evaluation of these 1980s race adjustments. We evaluated the relationship between AFP and race in a general population genetic screening cohort.

Targeted BRCA1/2 population screening among Ashkenazi Jewish individuals using a web-enabled medical model: An observational cohort study

PurposeThis study aimed to evaluate uptake and follow-up using internet-assisted population genetic testing (GT) for BRCA1/2 Ashkenazi Jewish founder pathogenic variants (AJPVs). MethodsAcross 4 cities in the United States, from December 2017 to March 2020, individuals aged ≥25 years with ≥1 Ashkenazi Jewish grandparent were offered enrollment. Participants consented and enrolled online with chatbot and video education, underwent BRCA1/2 AJPV GT, and chose to receive results from their primary care provider (PCP) or study staff. Surveys were conducted at baseline, at 12 weeks, and annually for 5 years. ResultsA total of 5193 participants enrolled and 4109 (79.1%) were tested (median age = 54, female = 77.1%). Upon enrollment, 35.1% of participants selected a PCP to disclose results, and 40.5% of PCPs agreed. Of those tested, 138 (3.4%) were AJPV heterozygotes of whom 21 (15.2%) had no significant family history of cancer, whereas 86 (62.3%) had a known familial pathogenic variant. At 12 weeks, 85.5% of participants with AJPVs planned increased cancer screening; only 3.7% with negative results and a significant family history reported further testing. ConclusionAlthough continued follow-up is needed, internet-enabled outreach can expand access to targeted GT using a medical model. Observed challenges for population genetic screening efforts include recruitment barriers, improving PCP engagement, and increasing uptake of additional testing when indicated.