Base by Base

️ Episode 153: Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits In this episode of PaperCast Base by Base, we explore a large skeletal muscle eQTL meta-analysis that integrates GTEx and FUSION data to pinpoint regulatory variants and genes underlying muscular and cardiometabolic traits. Study Highlights:Combining RNA-seq and whole-genome data from 1,002 individuals across two cohorts, the authors identified 18,818 conditionally distinct eQTL signals affecting 12,283 genes, with 35% of genes harboring multiple signals. Colocalization with 26 GWAS datasets yielded 2,252 signal pairs and nominated 1,342 candidate genes, and strikingly 22% of the colocalizations involved non‑primary eQTL signals while many mapped far from the nearest transcription start site. A focused multi‑tissue analysis for type 2 diabetes linked 309 of 862 tested signals to 551 genes across skeletal muscle, adipose, liver, and islet, representing 36% of T2D signals and exceeding the yield of any single tissue. The study also functionally validated a T2D‑linked variant at the INHBB locus, where the risk allele increased enhancer activity and aligned with higher gene expression in both muscle and adipose models. Conclusion:This work delivers a well‑powered skeletal muscle eQTL resource and shows how multi‑signal, multi‑tissue integration clarifies the molecular mechanisms and candidate targets underlying cardiometabolic disease. Reference:Wilson EP, Broadaway KA, Parsons VA, Vadlamudi S, Narisu N, Brotman SM, Currin KW, Stringham HM, Erdos MR, Welch R, Holtzman JK, Lakka TA, Laakso M, Tuomilehto J, Boehnke M, Koistinen HA, Collins FS, Parker SCJ, Scott LJ, Mohlke KL. Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits. The American Journal of Human Genetics. 2025;112:1–15. https://doi.org/10.1016/j.ajhg.2025.09.003 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 152: One-Well Multiplex ddPCR for Hereditary Alpha Tryptasemia In this episode of PaperCast Base by Base, we explore a validated single‑well multiplex digital droplet PCR (ddPCR) assay that reconstructs the TPSAB1 locus by quantifying α‑ and β‑tryptase copy numbers to diagnose hereditary alpha tryptasemia (HαT) in symptomatic patients. Study Highlights:The authors designed a triplex ddPCR assay that simultaneously measures α‑ and β‑tryptase copy numbers and an internal reference in one well, avoiding cross‑reactivity and excessive signal “rain” while achieving clear cluster separation and straightforward thresholds. In analytical validation across 281 cases, copy‑number calls tightly clustered around expected integers with an overall 99% prediction interval of 0.03 ± 0.27 copies and showed 100% concordance with a prior double‑well reference assay for all genotypes tested. In a clinical subcohort of 141 symptomatic patients without other causes of elevated tryptase, basal serum tryptase (BST) predicted HαT with an optimal cutoff of 9.2 ng/mL, yielding 98.1% sensitivity and 96.6% specificity. A strong gene–dose relationship was observed, with BST increasing by an average of 7.5 ng/mL for each additional α‑tryptase copy, and thresholds helped distinguish duplications from higher‑order α‑copy states. Conclusion:A simple, robust single‑well multiplex ddPCR enables accurate HαT genotyping and provides actionable BST thresholds to triage symptomatic patients for confirmatory testing. Reference:Alheraky A, Wierenga ATJ, Simpelaar A, Hesp LB, Minovic I, Bagheri N, Roozendaal C, Span LFR, Oude Elberink HNG, Kema IP, Mulder AB. Hereditary Alpha Tryptasemia: Validation of a Single‑Well Multiplex Digital Droplet PCR Assay in a Cohort of Symptomatic Patients. Clinical Chemistry. 2024;70(2):425–433. https://doi.org/10.1093/clinchem/hvad206 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Episode Slug: one-well-multiplex-ddpcr-for-hereditary-alpha-tryptasemia Keywords: hereditary alpha tryptasemia; TPSAB1 copy number; digital droplet PCR; basal serum tryptase; diagnostic cutoff Chapters (00:00:00) - Hereditary erypticemia: Solving the genetic puzzle(00:05:05) - Mastocytosis DNA test: Single Well Multiplex Digital(00:09:18) - How did the new single well test perform?(00:15:15) - Heidelberg Disease: The new test for hereditary alpha trypt

️ Episode 151: EQA of ctDNA Mutation Testing Across the COIN Consortium In this episode of PaperCast Base by Base, we explore how 16 Dutch laboratories evaluated their real‑world workflows for circulating tumor DNA (ctDNA) mutation testing across BRAF, EGFR, and KRAS using a coordinated external quality assessment within the COIN consortium. Study Highlights:The team distributed six plasma samples—three commercial references with predefined variants and three patient‑derived diagnostic leukapheresis samples—to participating labs, asking them to run their routine preanalytical and analytical pipelines, including ddPCR, small PCR panels, and next‑generation sequencing. Performance was scored on protocol adherence, overall detection, and precise genotyping, revealing broad variability in plasma input, extraction methods, and elution volumes and showing that only 38% of labs achieved a performance score above 0.90. Although 81% reached a 100% overall detection rate for the variants they assayed, clinically actionable mutations such as EGFR p.(S752_I759del), EGFR p.(N771_H773dup), and KRAS p.(G12C) were frequently mis‑genotyped, largely reflecting assay design limits. NGS approaches generally enabled more accurate variant‑level calls but carried a higher risk of false positives, while single‑target assays demonstrated sensitivity yet lacked breadth to cover all guideline‑relevant loci. Conclusion:Harmonizing preanalytical handling and selecting assays with adequate breadth and specificity are essential to deliver reproducible, clinically actionable liquid biopsy results in routine practice. Reference:van der Leest P, Rozendal P, Hinrichs J, van Noesel CJM, Zwaenepoel K, et al. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA‑Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium. Clinical Chemistry. 2024;70(5):759–767. https://doi.org/10.1093/clinchem/hvae014 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - Chopping Through the DNA of Cancer(00:03:18) - Commemorating the COIN Consortium(00:03:56) - The challenge of standardization in cancer DNA testing(00:07:56) - The EGFR Genotyping Study(00:10:59) - Liquid DNA standardization

️ Episode 150: Patrilineal segmentary systems and the post‑Neolithic Y‑chromosome bottleneck In this episode of PaperCast Base by Base, we explore a Nature Communications study that proposes a peaceful, socio‑cultural explanation for the sharp decline in male effective population size observed 3,000–5,000 years ago. Instead of widespread violence, the authors show that the dynamics of patrilineal segmentary systems—where lineages split and reproductive success varies between descent groups—can alone generate the Y‑chromosome bottleneck while female lineages continue to expand. Study Highlights:The team builds forward‑time simulations of villages structured by patrilocal residence and patrilineal descent, calibrating Y‑chromosome and mtDNA mutation rates and tracking effective population sizes over 100+ generations. They compare scenarios with random versus lineal fission of descent groups and incorporate empirically grounded variance in reproductive success between groups, with and without modeled violence. Lineal fission combined with inter‑group variance in reproductive success consistently produces a strong reduction in male effective population size, whereas violence alone or random fission has a much weaker effect. Bayesian skyline plots from simulated data reproduce a male‑specific bottleneck alongside continued growth of female effective size, and the timing aligns with post‑Neolithic shifts as agro‑pastoralism and patrilineal inheritance spread. Sensitivity analyses show the bottleneck strengthens as variance in reproductive success increases, while female‑to‑male Ne ratios can reach values comparable to those inferred from real data. Conclusion:A shift toward patrilineal, segmentary social organization with lineal fission and unequal reproductive success between descent groups may be sufficient to explain the post‑Neolithic Y‑chromosome bottleneck without invoking pervasive warfare. Reference:Guyon L, Guez J, Toupance B, Heyer E, Chaix R. Patrilineal segmentary systems provide a peaceful explanation for the post‑Neolithic Y‑chromosome bottleneck. Nature Communications. 2024;15:3243. https://doi.org/10.1038/s41467-024-47618-5 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - Why Human Genetics Hold the Secret to Mass Violence(00:05:29) - Social Inequality and Genetic Inequality(00:07:08) - The Social Structure and Lineal Fission(00:13:42) - Social structure explained the bottleneck in DNA diversity(00:15:52) - How social organization shaped the human genome

️ Episode 149: Cultural Hitchhiking and the Post‑Neolithic Y‑Chromosome Bottleneck In this episode of PaperCast Base by Base, we explore how patrilineal social structures and intergroup competition can reshape genetic diversity, offering a cultural explanation for the striking male‑specific bottleneck observed 5,000–7,000 years ago across the Old World. Study Highlights:The authors synthesize anthropological theory, population genomics, and mathematical modeling to test whether competition among patrilineal kin groups could drive a sharp reduction in Y‑chromosome diversity while leaving mitochondrial lineages relatively stable. They introduce an analytical Lotka–Volterra framework and a computational grid simulation to show that when descent groups are patrilineal and compete, entire Y‑chromosome clades can be lost at accelerated rates through cultural hitchhiking and drift. Simulations reproduce two key empirical signals seen in modern datasets: a bottleneck‑like collapse in male line diversity without requiring a demographic crash, and rapid, star‑like expansions of a few dominant Y lineages. Archaeogenetic patterns from post‑Neolithic farmer and pastoralist cultures further align with the model’s expectations, showing shallow coalescence and high Y‑line homogeneity within cultural groups across large geographies. Conclusion:By linking social organization to genetic patterns, this work reframes the post‑Neolithic Y‑chromosome bottleneck as a cultural phenomenon, sharpening how archaeogenetic signals can be interpreted to infer past social structure and conflict dynamics. Reference:Zeng, T. C., Aw, A. J., & Feldman, M. W. Cultural hitchhiking and competition between patrilineal kin groups explain the post‑Neolithic Y‑chromosome bottleneck. Nature Communications, 2018; 9:2077. https://doi.org/10.1038/s41467-018-04375-6 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Chapters (00:00:14) - The genetic crash of the Neoles(00:02:43) - The genetic bottleneck of the Neolithic(00:09:08) - How patrilineal DNA helped explain human societies(00:14:28) - Base by base science podcast

️ Episode 148: Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants In this episode of PaperCast Base by Base, we explore a comprehensive functional assessment of splice-site variants in CHEK2 using reporter minigenes, revealing how disrupted pre-mRNA splicing contributes to hereditary breast cancer risk and how these readouts can support clinical variant classification. Study Highlights:The authors screened 128 intron–exon boundary variants from large breast cancer cohorts with in silico tools and selected 52 candidates for minigene assays that collectively span all 15 CHEK2 exons.In transfected MCF-7 cells, 46 of the 52 variants impaired splicing, frequently abolishing the full-length transcript and generating a remarkably complex set of 89 annotated RNA isoforms through exon skipping, intron retention, and alternative splice-site usage. Several transcripts introduced premature termination codons consistent with predicted nonsense-mediated decay, while a minority preserved the open reading frame or altered the 5′UTR, illustrating diverse molecular consequences. A notable mechanistic finding was activation of a rare noncanonical TG acceptor site by variant c.684-2A>G, with exon 6 enhancer motifs mapped as critical for this atypical splice-site recognition.Incorporating minigene readouts into an ACMG/AMP-inspired Bayesian framework enabled tentative reclassification of 32 variants, including 27 as pathogenic or likely pathogenic and 5 as likely benign, while 20 remained VUS due to complex splicing profiles. Conclusion: Minigene-based splicing assays provide scalable, allele-specific functional evidence that can sharpen clinical interpretation of CHEK2 variants and should be integrated alongside population and case–control data in variant curation workflows. Reference: Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Esteban-Sánchez A, Lorca V, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Infante M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco-Sampedro EA. Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants. Clinical Chemistry. 2024;70(1):319–338. https://doi.org/10.1093/clinchem/hvad125 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Episode Slug: systematic-minigene-based-splicing-analysis-and-tentative-clinical-classification-of-52-chek2-splice-site-variants Keywords: CHEK2; splicing; minigene; variant classification; hereditary breast cancer Chapters (00:00:14) - First look at the genetic uncertainty in cancer screening(00:02:23) - Breast Cancer genetic screening, the QIQUE2 gene(00:04:19) - Breast cancer: the minigene approach(00:06:06) - Flip-flopping in splicing(00:08:46) - The pathogenicity of C6842AG

️ Episode 147: Comprehensive Annotation of Complete ABO Alleles and Resolution of ABO Variants In this episode of PaperCast Base by Base, we explore a groundbreaking study that introduces an improved long-read sequencing method to fully resolve ABO haplotypes, spanning from the 5′ to the 3′ untranslated regions. This work addresses a major gap in blood group genomics by delivering the most comprehensive annotation of complete ABO alleles to date. Study Highlights:Researchers analyzed specimens from 79 blood donors and 47 ABO variants using an optimized ultra-long-range PCR method combined with PacBio SMRT sequencing. They successfully amplified and sequenced the full 26.1 kb ABO gene without splicing, achieving complete coverage including the regulatory 5′ and 3′ UTRs. The study provided detailed haplotype sequences of predominant alleles in a Chinese population, revealing structural variations, recombination events, and previously unknown subtypes. Importantly, this method also resolved complex variants, including large deletions, chimeras, and intronic regulatory motifs, offering new insights into ABO allele diversity and molecular mechanisms. Conclusion:This comprehensive full-length ABO haplotype sequencing approach advances transfusion medicine by improving variant resolution, refining allele classification, and enabling more accurate genomic analysis for clinical and evolutionary applications. Reference:Ying Y, Zhang J, Hong X, Yuan W, Ma K, Huang X, Xu X, Zhu F. Comprehensive Annotation of Complete ABO Alleles and Resolution of ABO Variants by an Improved Full-Length ABO Haplotype Sequencing. *Clinical Chemistry*. 2025;71(4):510–519. https://doi.org/10.1093/clinchem/hvaf015 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - Base by Base: The mystery of blood types(00:01:27) - Full-length ABO haplotype sequencing(00:06:05) - Anatomy 5, Chinese genetic variation(00:06:54) - The structural variations of the ABO genome(00:09:38) - ULRPCR: The Bigger Alga

️ Episode 146: Automated and Decentralized Genomic Profiling of Plasma Cell-Free DNA in Solid Tumors In this episode of PaperCast Base by Base, we explore the clinical feasibility of an automated and decentralized cfDNA sequencing system designed to identify actionable and resistance alterations in advanced solid tumors. Study Highlights:Researchers evaluated plasma cfDNA from 298 patients with advanced cancers using the Oncomine Precision Assay GX and Genexus integrated sequencer. Sequencing success rates were higher for cfDNA compared to tumor tissue, and 50% of patients had detectable ctDNA mutations. Concordance between plasma and tumor results reached 72%, with detection influenced by tumor type, burden, and metastatic site. Plasma-only alterations were observed in 18% of patients, particularly in those previously treated with targeted therapies, underscoring cfDNA’s role in capturing tumor evolution. Conclusion:This decentralized approach demonstrates strong potential for expanding timely genomic profiling and improving access to precision oncology. Reference:Chan HT, Otaki M, Hayashi N, Fukada I, Chin YM, Fukuda N, Hosonaga M, Wang X, Yunokawa M, Shinozaki E, Yamaguchi K, Wakatsuki T, Kasuga A, Nakamura Y, Takahashi S, Low SK. Automated and Decentralized Genomic Profiling of Plasma Cell-Free DNA for Identification of Targetable and Resistance Alterations in Advanced Solid Tumors. Clinical Chemistry. 2025;71(6):700-712. https://doi.org/10.1093/clinchem/hvaf045 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - Decentralized liquid biopsy for advanced cancers(00:01:31) - Liquid biopsy vs. tissue profiling(00:04:04) - Immunity from the liquid biopsy(00:04:49) - The Covance DNA test(00:07:23) - The Match Between Tissue and Plasma(00:08:13) - The rapid plasma test for cancer...(00:11:31) - Plasma only mutations in cancer(00:15:05) - Base by base science

️ Episode 145: A Validated Highly Sensitive Microsatellite Instability Assay Identifies PMS2 Variants in CMMRD In this episode of PaperCast Base by Base, we explore a study that validates a next-generation sequencing-based highly sensitive microsatellite instability (hs-MSI) assay for the diagnosis of constitutional mismatch repair deficiency (CMMRD), a rare childhood-onset cancer predisposition syndrome. The work focuses on improving detection of PMS2 pathogenic variants, the most frequent but technically challenging cause of CMMRD. Study Highlights:The researchers applied the hs-MSI assay to a blinded cohort of 66 blood and 24 tumor samples from individuals with CMMRD and controls, demonstrating a sensitivity of 98.5% and specificity of 100% in detecting the syndrome. The hs-MSI results showed strong correlation with whole-genome low-pass instability scores (LOGIC/MMRDness) and identified distinct microsatellite indel patterns that differentiated PMS2 variant carriers with an accuracy of 0.997. Higher hs-MSI scores were also associated with earlier age of tumor onset, highlighting its potential role as a biomarker for cancer risk stratification. Conclusion:This validated hs-MSI assay provides a robust and clinically feasible tool to support CMMRD diagnosis, distinguish PMS2 involvement, and personalize surveillance strategies. Reference:Marín F, Canet-Hermida J, Bianchi V, Chung J, Wimmer K, Foulkes W, et al. A Validated Highly Sensitive Microsatellite Instability Assay Accurately Identifies Individuals Harboring Biallelic Germline PMS2 Pathogenic Variants in Constitutional Mismatch Repair Deficiency. *Clinical Chemistry*. 2024;70(5):737–746. https://doi.org/10.1093/clinchem/hvae027 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:00) - A revolutionary cancer diagnostic tool for CMMRD(00:03:39) - The genetic test for CMMRD(00:07:27) - HS MSI assay: 100% specificity and 99% sensitivity(00:10:24) - Immunity of CMMRD: a genotype specific fingerprint(00:13:51) - HS MSI score for CMMRD

️ Episode 144: Revised time estimation of the ancestral human chromosome 2 fusion In this episode of PaperCast Base by Base, we explore a study that revisits one of the most defining events in human evolution: the fusion that gave rise to chromosome 2. This work refines previous estimates and provides a clearer timeline for when this pivotal genomic change occurred. Study Highlights:The authors developed an improved algorithm to analyze biased clustered substitutions, allowing more precise dating of genomic events. By comparing the genomes of humans with those of chimpanzees and bonobos, they estimated that the chromosome 2 fusion took place around 0.9 million years ago, with a confidence interval of 0.4 to 1.5 million years. Their findings suggest that this chromosomal event happened more recently than earlier studies had proposed, and the results also provide insights into evolutionary distances among great apes. The approach highlights how computational methods can refine our understanding of human speciation and the genetic divergence from our closest relatives. Conclusion:This study provides a sharper view of when the human chromosome 2 fusion occurred, offering new insights into the timing of our evolutionary history. Reference:Poszewiecka B, Gogolewski K, Stankiewicz P, Gambin A. Revised time estimation of the ancestral human chromosome 2 fusion. BMC Genomics. 2022;23:616. https://doi.org/10.1186/s12864-022-08828-7 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ Chapters (00:00:14) - The moment that set Modern Humans apart from Great apes(00:02:33) - The HSA2 fusion event reconstruction(00:06:53) - The New Clock for Human Genome Dating(00:10:41) - UBCS: A More Precise Human Evolution Clock?(00:16:33) - Coming soon: Base by Base

️ Episode 143: The genetic history of the Southern Caucasus: 5,000 years of continuity despite high mobility In this episode of PaperCast Base by Base, we explore a comprehensive archaeogenomic study tracing 230 ancient individuals from Georgia and Armenia over 5,000 years, from the Bronze Age to the Early Middle Ages. The research investigates how extensive mobility and cultural interactions shaped the genetic landscape of the Southern Caucasus. Study Highlights:The analysis of genome-wide data revealed a remarkably persistent local gene pool across millennia, even as populations absorbed ancestry from Anatolia, Iran, and the Eurasian Steppe during the Middle to Late Bronze Age. Evidence of population growth and increased diversity emerged in urban centers of eastern Georgia, where individual ancestry outliers were most frequent. The study also examined 21 individuals with artificially deformed skulls, showing that while the practice arrived with nomadic Steppe groups, it was quickly adopted as a local cultural tradition. By integrating haplotype sharing and runs of homozygosity, the researchers uncovered contrasting social structures between urban hubs with high diversity and rural communities with stronger endogamy. Conclusion:This study demonstrates that despite high levels of mobility and external influences, the Southern Caucasus maintained a core genetic continuity that highlights the resilience of local populations while providing new insights into cultural and demographic shifts. Reference:Skourtanioti E, Jia X, Tavartkiladze N, Bitadze L, Shengelia R, Tushabramishvili N, Aslanishvili V, Gasparyan B, Kandel AW, Naumann D, et al. The genetic history of the Southern Caucasus from the Bronze Age to the Early Middle Ages: 5,000 years of genetic continuity despite high mobility. Cell. 2025 Sep 18;188(19):5278–5294. doi:10.1016/j.cell.2025.07.013 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 142: Specifications of the ACMG/AMP Guidelines for PALB2 Variant Interpretation In this episode of PaperCast Base by Base, we explore how the Hereditary Breast, Ovarian, and Pancreatic Cancer Variant Curation Expert Panel (HBOP VCEP) developed gene-specific ACMG/AMP guidelines for the interpretation of PALB2 germline sequence variants, a key gene in hereditary cancer syndromes. Study Highlights:The HBOP VCEP assembled an international team of experts to refine the 2015 ACMG/AMP framework specifically for PALB2, a tumor suppressor gene involved in homologous recombination repair. They systematically reviewed 28 evidence codes, advising against the use of 13, limiting six, and tailoring nine to account for PALB2-specific biology. These specifications were validated through the curation of 39 pilot variants, achieving 84% concordance with ClinVar entries and leading to the reclassification of several variants of uncertain significance. The work emphasized the rarity of pathogenic missense variation in PALB2, focusing instead on loss-of-function mechanisms and evidence-based population frequency cutoffs. Conclusion:These conservative, PALB2-specific guidelines enhance the accuracy and consistency of variant classification, improving genetic counseling and risk management for individuals with PALB2-related cancer predisposition. Reference:Richardson, M.E., Bishop, M.F.H., Holdren, M.A., de la Hoya, M., Spurdle, A.B., Tavtigian, S.V., Brannan, T., Young, C.C., Zec, L., Hiraki, S., Turnbull, C., Tischkowitz, M., Bernstein, K.A., Masson, J.-Y., McNulty, S.M., Pesaran, T., Monteiro, A.N., Walker, L.C., Foulkes, W.D., & Couch, F.J. (2025). Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline PALB2 sequence variants. *The American Journal of Human Genetics*, 112(10), 1–15. https://doi.org/10.1016/j.ajhg.2025.08.020 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 141: RetiGene, a comprehensive gene atlas for inherited retinal diseases In this episode of PaperCast Base by Base, we explore RetiGene, an expert-curated resource that consolidates genetic, transcriptomic, and functional information on inherited retinal diseases (IRDs). The study highlights the urgent need for a unified gene catalog to guide diagnosis and research in one of the most genetically heterogeneous groups of human disorders. Study Highlights:The authors identified and curated 470 genes strongly associated with IRDs, supported by extensive literature review, variant databases, and gene expression data. Another 196 genes were classified as candidate genes, while 17 were excluded due to insufficient or conflicting evidence. Phenotypic classification revealed associations across both syndromic and non-syndromic forms, with most genes showing autosomal recessive inheritance. Integration of bulk and single-cell RNA sequencing data revealed cell-type specificity of many genes, particularly in photoreceptors and retinal pigment epithelium, clarifying genotype-phenotype relationships. The database also distinguishes genes with solid evidence from those previously misattributed, providing a refined tool for diagnostics and research. Conclusion:RetiGene offers an updated, freely accessible gene atlas that improves genetic testing, supports functional studies, and enables future therapeutic development for inherited retinal diseases. Reference:Rivolta, C., Celik, E., Kamdar, D., Cancellieri, F., Kaminska, K., Ullah, M., Barberán-Martínez, P., Bouckaert, M., Cortón, M., Delanote, E., et al. (2025). RetiGene, a comprehensive gene atlas for inherited retinal diseases. *The American Journal of Human Genetics*, 112(10), 1–13. https://doi.org/10.1016/j.ajhg.2025.08.017 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 140: Landscapes of missense variant impact for human superoxide dismutase 1 In this episode of PaperCast Base by Base, we explore a large-scale functional analysis of missense variants in SOD1, a key gene implicated in amyotrophic lateral sclerosis (ALS). The study addresses the challenge of classifying variants of uncertain significance by systematically testing their functional impact across nearly all possible amino acid substitutions. Study Highlights:Using saturation mutagenesis combined with multiplexed yeast and human cell-based assays, researchers generated variant-effect maps covering 86% of all possible SOD1 missense variants. These maps measure both enzymatic activity and protein abundance, capturing functional effects that align with known biochemical features of SOD1. The results show that many variants exhibit damaging effects, while others remain tolerated, and importantly, the abundance assay provided new evidence to reclassify 41% of variants previously listed as uncertain. Structural and computational analyses further revealed insights into sequence-structure-function relationships, including metal binding, dimerization, and stability. Together, these findings demonstrate that large-scale variant-effect maps can provide critical evidence for clinical interpretation of SOD1 variants. Conclusion:This study highlights how systematic functional assays can accelerate variant classification in ALS and support more precise genetic diagnoses and therapeutic decisions. Reference:Axakova A, Ding M, Cote AG, Subramaniam R, Senguttuvan V, Zhang H, Weile J, Douville SV, Gebbia M, Al-Chalabi A, Wahl A, Reuter J, Hurt J, Mitchell AA, Fradette S, Andersen PM, van Loggerenberg W, Roth FP. Landscapes of missense variant impact for human superoxide dismutase 1. *Am J Hum Genet*. 2025 Oct 2;112(10):1-21. doi:10.1016/j.ajhg.2025.08.019 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

️ Episode 139: MosCoverY: A new method to estimate mosaic loss of Y chromosome from sequencing coverage data In this episode of PaperCast Base by Base, we explore the development of MosCoverY, a computational method designed to detect and quantify mosaic loss of the Y chromosome (mLOY) from exome and whole-genome sequencing data. This condition, the most common somatic mutation in men, is strongly linked with aging and several diseases. Study Highlights:The researchers introduced MosCoverY, a tool that focuses on single-copy genes of the Y chromosome and normalizes their coverage against carefully matched autosomal exons. They applied it to more than 212,000 male participants in the UK Biobank and demonstrated its accuracy by replicating associations of mLOY with age, smoking, mortality, and known germline loci. The method was also validated in tumor samples from The Cancer Genome Atlas, revealing variable prevalence of mLOY across cancer types. MosCoverY proved robust even at lower sequencing depths and can be applied to both large cohorts and single-sample analyses, making it versatile for population genetics and clinical research. Conclusion:MosCoverY provides a scalable and reliable approach to study mLOY in genomic datasets, opening opportunities for insights into age-related disease risk and male-specific health outcomes. Reference:Timonina V, Marchal A, Abel L, Cobat A, Fellay J. MosCoverY: A method to estimate mosaic loss of Y chromosome from sequencing coverage data. The American Journal of Human Genetics. 2025 Oct 2;112(1):1-11. doi:10.1016/j.ajhg.2025.08.016 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Keywords: mLOY, exome sequencing, whole-genome sequencing, aging, MosCoverY

️ Episode 138: Social exposome and brain health outcomes of dementia across Latin America In this episode of PaperCast Base by Base, we explore how a multidimensional social exposome across the lifespan—covering education, food insecurity, financial status, assets, access to healthcare, childhood labor, subjective socioeconomic status, childhood experiences, traumatic events, and relationships—relates to brain health and dementia outcomes in Latin America. The study analyzes 2,211 participants from Argentina, Brazil, Chile, Colombia, Mexico, and Peru, spanning healthy controls, Alzheimer’s disease, and frontotemporal lobar degeneration. Study Highlights:Researchers built a global multidimensional social exposome score using expert criteria, confirmatory factor analysis, and structural equation modeling, then evaluated its association with cognition, functional ability, neuropsychiatric symptoms, gray‑matter volume, and resting‑state connectivity. More adverse exposomes tracked with poorer cognition in healthy aging and with lower cognitive and functional performance plus higher neuropsychiatric symptoms in Alzheimer’s disease and frontotemporal lobar degeneration. The combined exposome measure outperformed single factors such as education or socioeconomic status proxies when predicting clinical–cognitive profiles. Brain analyses linked adverse exposomes to atrophy in frontal–temporo–limbic and cerebellar regions and to altered frontotemporal and limbic connectivity, suggesting cumulative social adversity burdens relevant neural systems. Conclusion:Integrating a multidimensional social exposome into dementia prevention and care can sharpen risk profiling and guide interventions that target social disparities across the lifespan. Reference:Migeot J, Pina‑Escudero SD, Hernandez H, Gonzalez‑Gomez R, Legaz A, Fittipaldi S, Resende E de PF, Duran‑Aniotz C, Avila‑Funes JA, Behrens MI, Bruno MA, Cardona JF, Custodio N, García AM, Godoy ME, Hu K, Lanata S, Lawlor B, Lopera F, Maito MA, Matallana DL, Miller B, Miranda JJ, Okada de Oliveira M, Reyes P, Santamaria‑Garcia H, Slachevsky A, Sosa AL, Takada LT, Torres JM, Vanneste S, Valcour V, Wen O, Yokoyama JS, Possin KL, Ibanez A. Social exposome and brain health outcomes of dementia across Latin America. Nature Communications. 2025;16:8196. https://doi.org/10.1038/s41467-025-63277-6 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/   On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 137: Rethinking RNA-binding proteins: Riboregulation challenges prevailing views In this episode of PaperCast Base by Base, we explore how a sweeping expansion of the RNA-binding proteome has reframed long‑held assumptions about RNA–protein interactions, spotlighting ‘non‑canonical’ RBPs and the emerging concept of riboregulation—RNA directly regulating protein function. Study Highlights:The authors synthesize discovery platforms that tripled the number of candidate RBPs, including UV crosslinking–based interactome capture (RIC/eRIC), silica‑based workflows (TRAPP/2C), and organic‑phase methods (OOPS/XRNAX), together with mass spectrometry to map RNA‑binding regions across the proteome. They show that intrinsically disordered regions and classical metabolite‑binding folds such as Rossmann domains frequently mediate RNA contacts, helping explain why many metabolic enzymes and signaling proteins appear in RBP datasets. Mechanistic case studies reveal RNA acting as a regulator of protein complexes and enzyme activity, exemplified by vtRNA1‑1 control of p62 oligomerization, SHMT1 inhibition by the SHMT2 5′UTR, ENO1 crowd‑control by UTR ligands, and circACC1 scaffolding of AMPK. The review outlines validation workflows and open questions to separate functional riboregulation from chance binding and artifacts, emphasizing orthogonal assays, target identification, and structure‑guided mutants. Conclusion:Together, these insights argue that riboregulation is likely widespread and clinically relevant, opening new routes to interrogate cell biology and to design therapeutic strategies that target RNA–protein interfaces. Reference:Hentze, M. W., Sommerkamp, P., Ravi, V., & Gebauer, F. (2025). Rethinking RNA-binding proteins: Riboregulation challenges prevailing views. Cell, 188, 4811–4822. https://doi.org/10.1016/j.cell.2025.06.021 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 136: Gene Context Drift Identifies Drug Targets to Mitigate Cancer Treatment Resistance In this episode of PaperCast Base by Base, we explore RECODR, a graph‑embedding pipeline that reads single‑cell and single‑nucleus transcriptomes as co‑expression networks to quantify “gene context drift” during therapy and expose druggable vulnerabilities that drive relapse across aggressive cancers. Study Highlights:RECODR constructs co‑expression graph networks from sc/snRNA‑seq data and uses Node2Vec/Word2Vec embeddings to score how each gene’s neighborhood shifts between normal, tumor, and treatment states, revealing resistance drivers that expression level alone misses. In a choroid plexus carcinoma mouse model, context drift pinpointed DNA‑damage response dependencies, nominating ATM as a primary vulnerability and predicting that PARP1 would be inactive in untreated tumors but synergistic after ATM inhibition or radiation. Preclinical trials validated these predictions: the brain‑penetrant PARP1 inhibitor AZD9574 enhanced the ATM inhibitor AZD1390 or radiotherapy in relapsed tumors, while dasatinib—prioritized from an immune‑like resistance program—mitigated failure of the combined ATM inhibitor–radiation regimen when timed to resistant outgrowth. Applying RECODR to paired patient medulloblastoma and triple‑negative breast cancer profiles uncovered relapse‑associated context drift programs and proposed repurposable, blood–brain‑barrier–penetrant drugs tailored to subtype‑specific resistance biology. Conclusion:Gene context drift provides a practical framework to anticipate resistance pathways and design precisely timed combination schedules that remain effective where single agents fail. Reference:Jassim A, Nimmervoll BV, Terranova S, et al. Gene context drift identifies drug targets to mitigate cancer treatment resistance. Cancer Cell. 2025;43(9):1608–1621. doi:10.1016/j.ccell.2025.06.005. License:This episode is based on an open‑access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one‑time or monthly donation here: https://basebybase.castos.com/

️ Episode 135: Global impact of micronutrients in modern human evolution In this episode of PaperCast Base by Base, we explore how dietary micronutrients have influenced modern human evolution. The study investigates the role of essential minerals in shaping genetic adaptation and highlights the health risks posed by imbalances in micronutrient availability worldwide. Study Highlights:Researchers analyzed 276 genes linked to 13 micronutrients across 40 diverse human populations. Using whole-genome data and evolutionary simulations, they identified widespread signatures of positive selection in genes associated with nutrient uptake, metabolism, and regulation. Their findings suggest that deficiencies in elements such as selenium, iodine, iron, and zinc have repeatedly driven local adaptation across global populations. The study also reveals that oligogenic selection, acting on multiple genes at once, may have been a common mechanism of adaptation. Importantly, patterns of selection often correspond with geographic differences in soil composition and diet, underscoring the deep link between human genetics and the environment. Conclusion:This research shows that micronutrient deficiencies have been a powerful selective force in human history and remain relevant today as soil depletion and climate change continue to shape global health risks. Reference:Rees, J., Castellano, S., & Andrés, A. M. (2025). Global impact of micronutrients in modern human evolution. *The American Journal of Human Genetics*, 112, 1–24. https://doi.org/10.1016/j.ajhg.2025.08.005 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

️ Episode 134: Single-Cell Maps Link Intestinal Metaplasia to Esophageal Adenocarcinoma Risk In this episode of PaperCast Base by Base, we explore how single-cell RNA sequencing of Barrett’s esophagus (BE), esophageal adenocarcinoma (EAC), and matched normal tissues reveals which cell types carry germline-linked risk and shape progression toward cancer. Study Highlights:The authors profiled epithelial, stromal, endothelial, and immune cells with 10x scRNA-seq and integrated genome-wide association data using partitioned heritability to map risk to specific cell types. They show that EAC development is driven more by local cellular programs than BE, with intestinal metaplasia cells—goblet cell–like cells expressing the intestinal stem cell marker OLFM4—emerging as pivotal in the transition toward malignancy. Tumor clusters displayed patient-specific copy-number profiles, and gene set analyses suggested that columnar cell differentiation programs, particularly within intestinal metaplasia, are closely tied to EAC risk. Fibroblast and endothelial subtypes also carried enriched risk signals, while plasmacytoid dendritic cells and memory CD4 T cells were linked to BE risk, highlighting immune involvement in the metaplastic stage. Conclusion:Linking GWAS risk loci to single-cell expression programs points to intestinal metaplasia and columnar differentiation states as key targets for early prediction and intervention in EAC. Reference:Wenzel MC, Dasmeh P, Plum PS, Giel A-S, Hoppe S, Franitza M, Jonas C, Thieme R, Zhao Y, Heider D, Palles C, Fitzgerald RC, Bruns CJ, Buettner R, Quaas A, Gockel I, Maj C, Chon S-H, Schumacher J, Hillmer AM. Single-cell analysis of Barrett’s esophagus and carcinoma reveals cell types conferring risk via genetic predisposition. Cell Genomics. 2025;5:100980. https://doi.org/10.1016/j.xgen.2025.100980 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/ On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.