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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

00:23:42

309: LASI-DAD 2,680-sample WGS panel boosts LD maps,...

Base by Base ·

2026/03/06

Li Z et al., Human Genetics and Genomics Advances. 7 ( - LASI-DAD 30× whole-genome sequencing of 2,680 Indian participants produced a 69.5M-variant LD panel that improves genotype imputation accuracy and PRS performance for Indian populations. Study Highlights:Using 30× WGS of 2,680 LASI-DAD participants, the authors constructed an LD lookup panel (69.5 million variants), phased with Eagle2.4, and identified LD structure with LDetect and Big-LD. They

en-us

00:23:42

309: LASI-DAD 2,680-sample WGS panel boosts LD maps,...

Base by Base ·

2026/03/06

Li Z et al., Human Genetics and Genomics Advances. 7 ( - LASI-DAD 30× whole-genome sequencing of 2,680 Indian participants produced a 69.5M-variant LD panel that improves genotype imputation accuracy and PRS performance for Indian populations. Study Highlights:Using 30× WGS of 2,680 LASI-DAD participants, the authors constructed an LD lookup panel (69.5 million variants), phased with Eagle2.4, and identified LD structure with LDetect and Big-LD. They

en-us

00:22:25

308: PANDORA-seq reveals conserved rsRNA length shift...

Base by Base ·

2026/03/05

Shi J et al., The EMBO Journal - PANDORA-seq profiling of mouse and human sperm heads identifies a conserved rsRNA length shift with age and a tsRNA/rsRNA 'aging cliff' that reprograms embryonic transcripts. Study Highlights:Using PANDORA-seq on C57BL/6J mouse sperm (intact and de-membranated heads) across five age groups and two independent human sperm cohorts, the authors identify a sharp tsRNA/rsRNA "aging cliff" in mice between 50–70 weeks and a

en-us

00:27:44

307: SNIPE membrane nuclease cleaves phage λ DNA...

Base by Base ·

2026/03/04

Saxton DS et al., Nature - In E. coli, the membrane-bound nuclease SNIPE directly cleaves incoming phage λ DNA during genome injection, blocking infection via ManYZ and tape-measure protein interactions. Study Highlights:In Escherichia coli, the membrane-anchored protein SNIPE was shown to block phage λ by directly cleaving DNA during genome injection. The authors combined radiolabelled 32P phage DNA assays, time-lapse CFP-ParB/ParS microscopy, TurboID

en-us

00:27:44

307: SNIPE membrane nuclease cleaves phage λ DNA...

Base by Base ·

2026/03/04

Saxton DS et al., Nature - In E. coli, the membrane-bound nuclease SNIPE directly cleaves incoming phage λ DNA during genome injection, blocking infection via ManYZ and tape-measure protein interactions. Study Highlights:In Escherichia coli, the membrane-anchored protein SNIPE was shown to block phage λ by directly cleaving DNA during genome injection. The authors combined radiolabelled 32P phage DNA assays, time-lapse CFP-ParB/ParS microscopy, TurboID

en-us

00:25:09

306: SAXO6 loss-of-function in photoreceptor cilia...

Base by Base ·

2026/03/03

Moye AR et al., The American Journal of Human Genetics - Biallelic loss-of-function variants in SAXO6, a microtubule inner protein of photoreceptor cilia, cause late-onset retinal dystrophy by destabilizing axonemal microtubules. Study Highlights:The study analyzed human patients with late-onset recessive retinal dystrophy and combined genetic sequencing (WES/WGS and long-read RNA) with high-resolution imaging and proteomics. Iterative ultrastructure

en-us

00:22:24

305: Human cis-regulatory variants dissected by MPRA...

Base by Base ·

2026/03/02

Siraj L et al., Nature - Using MPRA in five human cell types, the authors assayed 221,412 fine-mapped variants and identified 13,121 trait-associated regulatory variants (TARVs), mapping mechanisms at single-nucleotide resolution. Study Highlights:The study assayed 221,412 fine-mapped human GWAS and eQTL variants using a massively parallel reporter assay (MPRA) across five cell lines and performed saturation mutagenesis on 136 TARVs. MPRA identified

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00:18:13

304: Patrilineal Y‑chromosome drive in a Utah...

Base by Base ·

2026/03/02

Baldwin-Brown JG et al., Annual Review of Ecology and Systematics - Bayesian analysis of 76,445 Utah Population Database pedigrees identifies a patrilineal Y‑chromosome lineage producing a 2:1 male bias, consistent with segregation distortion. Study Highlights:We analyzed 76,445 anonymized human pedigrees from the Utah Population Database using a Bayesian pedigree-propagation algorithm (Warp), complemented by transmission disequilibrium testing,

en-us

00:29:00

303: Short-read sequencing and genome skimming for...

Base by Base ·

2026/02/28

Bleidorn C et al., Trends Genet - This review shows how short-read shotgun sequencing and genome skimming recover organellar genomes, estimate genome size and repeat content, and enable scalable biodiversity monitoring. Study Highlights:The authors review applications across eukaryotic biodiversity, museum specimens, bulk samples and eDNA using short-read shotgun sequencing and genome skimming. They detail assembly-free and mapping-based bioinformatic

en-us

00:29:00

303: Short-read sequencing and genome skimming for...

Base by Base ·

2026/02/28

Bleidorn C et al., Trends Genet - This review shows how short-read shotgun sequencing and genome skimming recover organellar genomes, estimate genome size and repeat content, and enable scalable biodiversity monitoring. Study Highlights:The authors review applications across eukaryotic biodiversity, museum specimens, bulk samples and eDNA using short-read shotgun sequencing and genome skimming. They detail assembly-free and mapping-based bioinformatic

en-us

00:13:58

302 auf Deutsch: SMN1/SMN2-Spleißen und Mechanismen...

Base by Base ·

2026/02/27

Ein Hommage-Dossier, das die wissenschaftliche Laufbahn von Prof. Brunhilde Wirth würdigt und Arbeiten zum alternativen Spleißen von SMN1/SMN2 hervorhebt. Im Fokus stehen Studien aus der molekularen Genetik und funktionelle Assays, die die Auswirkungen von Varianten bei SMA aufgeklärt haben. Studien-Highlights: Dieses Dossier beleuchtet jahrzehntelange Arbeit in der Humangenetik und zur spinalen Muskelatrophie und betont insbesondere Studien zu SMN1 und

en-us

00:13:58

302 auf Deutsch: SMN1/SMN2-Spleißen und Mechanismen...

Base by Base ·

2026/02/27

Ein Hommage-Dossier, das die wissenschaftliche Laufbahn von Prof. Brunhilde Wirth würdigt und Arbeiten zum alternativen Spleißen von SMN1/SMN2 hervorhebt. Im Fokus stehen Studien aus der molekularen Genetik und funktionelle Assays, die die Auswirkungen von Varianten bei SMA aufgeklärt haben. Studien-Highlights: Dieses Dossier beleuchtet jahrzehntelange Arbeit in der Humangenetik und zur spinalen Muskelatrophie und betont insbesondere Studien zu SMN1 und

en-us

00:24:12

302: SMN1/SMN2 splicing and last-exon mechanisms —...

Base by Base ·

2026/02/26

A Tribute Dossier Celebrating the Scientific Career of Prof. Brunhilde Wirth highlighting SMN1/SMN2 alternative splicing studies using molecular genetics and functional assays that clarified variant effects in SMA. Study Highlights:This dossier reviews decades of work in human genetics and spinal muscular atrophy, emphasizing studies of SMN1 and SMN2. Key methods included molecular genetics, splicing analysis, protein expression measurements, and

en-us

00:18:12

302: SMN1/SMN2 splicing and last-exon mechanisms —...

Base by Base ·

2026/02/26

A Tribute Dossier Celebrating the Scientific Career of Prof. Brunhilde Wirth highlighting SMN1/SMN2 alternative splicing studies using molecular genetics and functional assays that clarified variant effects in SMA. Study Highlights:This dossier reviews decades of work in human genetics and spinal muscular atrophy, emphasizing studies of SMN1 and SMN2. Key methods included molecular genetics, splicing analysis, protein expression measurements, and

en-us

00:20:53

301: Biobank Mendelian randomization prioritizes...

Base by Base ·

2026/02/25

Ferolito BR et al., Human Genetics and Genomics Advances. 7 ( - Meta-analysis of MVP, UK Biobank and FinnGen with Mendelian randomization using eQTL/pQTL instruments implicates 6,447 genes and 69,669 causal gene-trait links. Study Highlights:The authors meta-analyzed GWAS from MVP, UK Biobank, and FinnGen across 2,003 harmonized phenotypes and used cis-eQTLs and cis-pQTLs from GTEx, eQTLGen, ARIC, Fenland, and deCODE to perform two-sample Mendelian

en-us

00:20:53

301: Biobank Mendelian randomization prioritizes...

Base by Base ·

2026/02/25

Ferolito BR et al., Human Genetics and Genomics Advances. 7 ( - Meta-analysis of MVP, UK Biobank and FinnGen with Mendelian randomization using eQTL/pQTL instruments implicates 6,447 genes and 69,669 causal gene-trait links. Study Highlights:The authors meta-analyzed GWAS from MVP, UK Biobank, and FinnGen across 2,003 harmonized phenotypes and used cis-eQTLs and cis-pQTLs from GTEx, eQTLGen, ARIC, Fenland, and deCODE to perform two-sample Mendelian

en-us

00:21:48

300: Population-scale WGS links MHC class II antigen...

Base by Base ·

2026/02/24

Nyeo SS et al., Nature - Population-scale WGS reanalysis quantifies persistent EBV DNA and shows MHC class II–mediated antigen presentation predicts EBV DNAemia and links to autoimmune and respiratory disease. Study Highlights:Using whole-genome sequencing from UK Biobank (n≈490,560) and All of Us (n≈245,394), the authors extracted chrEBV-mapping reads, masked low-mappability regions, and defined EBV DNAemia (>1.2 genomes per 10^4 cells) in 9.7–11.9%

en-us

00:21:15

299: UFM1 loss and R81C mutation disrupt neuronal...

Base by Base ·

2026/02/23

Perdigão C et al., EMBO Molecular Medicine - In mouse neurons, UFM1 loss or UFM1-R81C expression reduces protein translation, triggers ER stress and PERK activation, impairing dendrite and synapse development. Study Highlights:Using murine UFM1-deficient neurons generated by conditional knockout and CRISPR/Cas9 in vivo manipulations and lentiviral rescue, the study combined FUNCAT, puromycin labeling, patch-clamp electrophysiology, RNA-seq, mass

en-us

00:20:16

298: Bi-allelic FSD1L variants in retinitis...

Base by Base ·

2026/02/22

Lin S et al., The American Journal of Human Genetics 113, 1–11 ( - Bi-allelic FSD1L variants cause retinitis pigmentosa; FSD1L localizes to the photoreceptor axoneme and a deep intronic deletion abolishes retina-enriched exon 10b inclusion. Study Highlights:In human and mouse retinal tissues and six affected individuals from four families, exome/genome sequencing identified bi-allelic ultra-rare FSD1L variants associated with retinitis pigmentosa

en-us

00:20:38

296: snaR-A ncRNA antagonizes U2 snRNP SF3B2 to drive...

Base by Base ·

2026/02/21

Zhou S et al., Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. Nature Communications - snaR-A noncoding RNA interacts with U2 snRNP subunit SF3B2 and nuclear speckles, increasing intron retention and promoting proliferation in human cancer-relevant cells. Study Highlights:Using human cell lines (HEK293T, A549, THP-1) and tumor chromatin data, the authors combined biotinylated

en-us

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