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PODCAST

Base by Base

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

science life sciences

All Episodes

00:20:15

162: Spatially Resolved microRNA Expression in...

Base by Base ·

2025/10/09

️ Episode 162: Spatially Resolved microRNA Expression in Tissues: Technologies, Challenges, and Opportunities In this episode of PaperCast Base by Base, we explore how emerging “spatial miRNomics” methods map microRNA expression directly within intact tissues, revealing cell- and region-specific regulatory patterns that bulk and even single-cell assays can miss. Study Highlights:This review charts the field from established singleplex imaging with LNA

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00:20:55

161: Decoding Genomic Landscapes of Introgression

Base by Base ·

2025/10/08

️ Episode 161: Decoding Genomic Landscapes of Introgression In this episode of PaperCast Base by Base, we explore how modern population genetics dissects the genomic footprints of introgression across species, reviewing summary statistic approaches, probabilistic modeling, and supervised learning, and showing how these methods reveal adaptive and ghost introgression and the functional roles of introgressed loci. Study Highlights:The authors organize the

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00:15:36

160: The Long‑Read Leap in Single‑Cell Omics

Base by Base ·

2025/10/07

️ Episode 160: The Long‑Read Leap in Single‑Cell Omics In this episode of PaperCast Base by Base, we explore how long‑read, single‑molecule sequencing has collided with single‑cell technologies to illuminate “dark” regions and events in the genome, epigenome, and transcriptome that short reads routinely miss. Study Highlights:This review maps the rapid maturation of Pacific Biosciences and Oxford Nanopore platforms alongside single‑cell methods, showing

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00:15:56

159: The Untapped Potential of Short‑Read Sequencing...

Base by Base ·

2025/10/06

️ Episode 159: The Untapped Potential of Short‑Read Sequencing in Biodiversity Research In this episode of PaperCast Base by Base, we explore how modern short‑read sequencing and genome skimming are reshaping biodiversity science—from rapid species identification and biomass estimation to scalable phylogenomics and holobiont studies—while keeping costs and sample requirements low. Study Highlights:This review synthesizes how low‑coverage short‑read data

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00:22:35

158: Interruptions in Repeat Expansion Diseases: How...

Base by Base ·

2025/10/05

️ Episode 158: Interruptions in Repeat Expansion Diseases: How Are They Gained and Lost? In this episode of PaperCast Base by Base, we explore how small sequence changes—“interruptions”—within expanded tandem repeats shape the onset and severity of repeat expansion disorders, and a new mechanistic model that may explain how these interruptions are gained and lost across generations. Study Highlights:Interruptions within repeat tracts can dampen somatic

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00:15:23

158: Interruptions in Repeat Expansion Diseases: How...

Base by Base ·

2025/10/05

️ Episode In this episode of PaperCast Base by Base, we explore how small sequence changes—“interruptions”—within expanded tandem repeats shape the onset and severity of repeat expansion disorders, and a new mechanistic model that may explain how these interruptions are gained and lost across generations. Study Highlights:Interruptions within repeat tracts can dampen somatic expansion and shift clinical trajectories, helping to explain variability in

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00:12:53

157: Synthetic gametes and the non-identity problem:...

Base by Base ·

2025/10/04

️ Episode 157: Synthetic gametes and the non-identity problem: the babies of tomorrow In this episode of PaperCast Base by Base, we explore how synthetic DNA technologies may enable the creation of synthetic gametes and why this possibility forces a rethinking of identity, harm, and responsibility in human reproduction. Study Highlights:The authors argue that while building a full human genome remains infeasible today, engineering haploid genomes for

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00:17:07

156: RAEFISH: Sequencing-free whole-genome spatial...

Base by Base ·

2025/10/03

️ Episode 156: RAEFISH: Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution In this episode of PaperCast Base by Base, we explore RAEFISH, a reverse-padlock amplicon-encoding FISH method that delivers whole-transcriptome imaging at single-molecule resolution without sequencing. The study demonstrates genome-scale coverage across cells and intact tissues and extends to direct readout of CRISPR guide RNAs, enabling

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00:15:53

155: EIF3A/EIF3B Loss-of-Function: A...

Base by Base ·

2025/10/02

️ Episode 155: EIF3A/EIF3B Loss-of-Function: A Cardiocraniofacial Neurodevelopmental Syndrome In this episode of PaperCast Base by Base, we explore how loss-of-function variants in EIF3A and EIF3B—core components of the eIF3 translation initiation complex—cause a multisystem disorder marked by congenital heart defects, craniofacial differences, and mild neurodevelopmental features. The study brings clinical genetics together with functional zebrafish

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00:20:05

154: Multiple-testing corrections in selection scans...

Base by Base ·

2025/10/01

️ Episode 154: Multiple-testing corrections in selection scans using identity-by-descent segments In this episode of PaperCast Base by Base, we explore how Temple and Browning develop principled genome-wide significance thresholds for IBD-based scans of recent positive selection by explicitly modeling correlation along the genome. Study Highlights:The authors model standardized IBD-rate scan statistics as an Ornstein–Uhlenbeck process and derive both an

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00:15:13

153: Skeletal muscle eQTL meta-analysis implicates...

Base by Base ·

2025/09/30

️ 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,

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00:16:53

152: One-Well Multiplex ddPCR for Hereditary Alpha...

Base by Base ·

2025/09/29

️ 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

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00:16:21

151: EQA of ctDNA Mutation Testing Across the COIN...

Base by Base ·

2025/09/28

️ 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

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00:16:21

151: EQA of ctDNA Mutation Testing Across the COIN...

Base by Base ·

2025/09/28

️ 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

en-us

00:17:52

150: Patrilineal segmentary systems and the...

Base by Base ·

2025/09/27

️ 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

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00:15:04

149: Cultural Hitchhiking and the Post‑Neolithic...

Base by Base ·

2025/09/26

️ 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

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00:14:44

148: Systematic Minigene-Based Splicing Analysis and...

Base by Base ·

2025/09/25

️ 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

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00:15:37

147: Comprehensive Annotation of Complete ABO Alleles...

Base by Base ·

2025/09/24

️ 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

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00:15:56

146: Automated and Decentralized Genomic Profiling of...

Base by Base ·

2025/09/23

️ 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

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00:16:59

145: A Validated Highly Sensitive Microsatellite...

Base by Base ·

2025/09/22

️ 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

en-us

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