CD Genomics

10/13/2026

🧬 11,692 genes silenced. 2.5 million single cells profiled. A genome-scale CRISPRi atlas of human iPSCs is now public.

A Nature Biotechnology study from UC San Diego (Nourreddine, Doctor et al., July 2026) applied CRISPR interference to virtually every expressed gene in human induced pluripotent stem cells, reading out each perturbation with pooled single-cell RNA sequencing.

Highlights:

✔ A perturbation-correlation map that reconstructs how iPSC transcriptomic states are organized — protein complexes emerge directly from correlated knockdown phenotypes ✔ New regulators validated experimentally: ZBTB41 (metabolism), RNF7 (pluripotency, alongside OCT4), DBR1 (A-to-I RNA editing via lariat RNA metabolism) ✔ Fully open: interactive browser, raw data, and the PASTA analysis pipeline

For virtual cell models and cell-fate engineering, this is reference-grade data — and a template for sharing perturbation atlases.

📄 Open access: https://doi.org/10.1038/s41587-026-03199-w

A transcriptional regulatory map of pluripotent stem cells is generated by CRISPR screening.

10/13/2026

📚 Customer publication spotlight:

A genome-wide CRISPR/Cas9 screen in haploid human embryonic stem cells identified ATF7IP as a key suppressor of paternal imprinting — and the DNA methylation maps that anchored the mechanism came from CD Genomics.

How do human embryos maintain imprinting marks through global demethylation? Bar et al. (Hebrew University of Jerusalem, Nature Communications, 2021) tackled it with a genome-wide knockout screen in haploid hESCs, where loss of imprinting at the single maternal allele is scorable by reporter.

🔬 For this study, the authors used reduced representation bisulfite sequencing (RRBS) — library preparation and sequencing provided by CD Genomics — to profile methylation at imprinting control regions across screened conditions.

The findings: ATF7IP suppresses paternal-expression genes like PEG10 via H3K9me3, linking imprinting maintenance to histone modification — with ZMYM2 as an additional regulator.

📄 Open access: https://doi.org/10.1038/s41467-021-26949-7

Genetic imprinting ensures monoallelic gene expression critical for normal embryonic development. Here the authors take advantage of human haploid parthenogenic embryonic stem cells lacking paternal alleles to identify, by genome-wide screening, factors involved in the regulation of imprinted genes.

10/13/2026

💉 The RNA you're looking for may not be in cells — it's in transit.

Exosomes shuttle miRNA, mRNA, and lncRNA between cells, and they're accessible in serum, plasma, and urine. For biomarker and cell-communication research, that circulating cargo is often the most clinically relevant transcriptome.

It's also technically hard: low input, no ribosomal peaks, contamination-prone isolations. CD Genomics' exosomal RNA sequencing service is built for it:

✔ Exosome isolation from serum/plasma (≥1 mL), urine, or culture supernatant ✔ RNA QC: total RNA ≥100 ng, RIN ≥6 ✔ Small RNA & total-RNA libraries on Illumina/MGI platforms (~10 Gb/sample) ✔ Analysis: miRNA/lncRNA/mRNA quantification, differential expression, GO/KEGG pathways

Non-invasive and repeatable — ideal for longitudinal treatment-response and disease-progression monitoring where tissue biopsies aren't feasible. Studies of exosome-mediated cell communication and liquid-biopsy biomarker discovery both fit the workflow.

📄 Details: https://www.cd-genomics.com/exosomal-rna-sequencing.html

10/13/2026

🧬 A pooled CRISPR screen is only as good as its readout.

Pooled screens compress thousands of perturbations into one flask — but hits only surface if sgRNA abundance is amplified, sequenced, and modeled correctly. Library PCR dropouts become false "essential genes"; under-sequencing buries real hits.

CD Genomics' CRISPR screen sequencing service handles the readout end:

✔ PCR amplification of sgRNA cassettes from genomic DNA with library-wide coverage ✔ Illumina HiSeq PE150 or PE300 matched to your screen design ✔ MAGeCK analysis: sgRNA abundance, fold changes, gene-level hit ranking ✔ Input: 5×10⁶ cells or ≥1.5 μg gDNA per condition

You get a statistically scored, ranked gene list — ready for pathway interpretation in drug target discovery, resistance mechanism studies, and functional genomics projects.

Already have a screen design in mind? Bring us your library size and selection scheme, and we'll scope the sequencing and analysis plan around it.

📄 Details: https://www.cd-genomics.com/crispr-screen-sequencing.html

10/08/2026

Pathogenic germline variants raise pediatric cancer risk 12-fold

A new Nature Medicine study followed tens of thousands of children who had clinical exome sequencing — and quantified what germline findings mean for cancer risk in early childhood.

Wang and colleagues analyzed data from 75,602 children under age three referred for genetic testing, focusing on 139 cancer-predisposition genes. Among 411 children who developed tumors, 32.6% carried pathogenic germline variants — most often in NF1, TSC2, RB1 and WT1.

The prospective follow-up stands out: among 64,187 children who were tumor-free at baseline, carriers developed malignant tumors at 3.23 per 1,000 person-years — about 12-fold higher than children with other variant classes.

Penetrance varied by gene, too: RB1 variants led to retinoblastoma in 90.5% of carriers, while WT1-linked Wilms tumor penetrance was around 52%.

For clinical genetics and pediatric oncology teams, the takeaway is clear: early germline findings should trigger genetic counseling and proactive tumor surveillance in young carriers.

Read the full paper (open access): https://doi.org/10.1038/s41591-026-04423-5

10/08/2026

How RNA-seq untangled self-compatibility and oil biosynthesis in Noug

Noug (Guizotia abyssinica) is an underutilized oilseed crop with real agronomic potential — but until recently, its genetics remained largely out of reach for breeders.

A new transcriptomics study tackled three traits that matter most for noug improvement: self-compatibility, flowering time, and oil biosynthesis.

Gebeyehu and colleagues extracted high-quality RNA and performed transcriptome sequencing to build a gene-expression atlas across tissues and developmental stages. For this study, the authors used RNA sequencing and analysis provided by CD Genomics.

The analysis mapped candidate genes and pathways — including lipid biosynthesis and reproductive development regulators — giving breeders a molecular entry point into a crop that has long been genetically obscure.

For teams working on non-model species, this case shows how a well-executed transcriptome can turn an orphan crop into a tractable breeding target.

Read the full paper: https://doi.org/10.1038/s41598-025-18728-x

Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia that contributes significantly to local edible oil production and is a good protein source in animal feed. Despite its agronomic importance, the molecular basis of key agronomic traits, such as self-compatibility, photo...

10/08/2026

NGS-Based Pathogen Detection for Genomic Surveillance

qPCR is fast, but it only detects what you already target. For outbreak tracing, antimicrobial resistance monitoring, or mixed infections, researchers often need full genomic context — strain identity, resistance genes, and phylogenetic placement.

CD Genomics provides pathogen detection and sequencing services based on capture NGS and amplicon sequencing:

— HBV, HPV, and EBV capture sequencing — Targeted pathogen capture sequencing (tNGS) — Gut microbiome profiling by 16S rRNA sequencing

The workflow supports DNA and RNA pathogens across bacteria, viruses, fungi, and parasites, with custom capture design, low-input samples, and downstream variant and resistance-gene analysis.

For transmission dynamics, complex infection profiling, and pathogen genomic databases, NGS delivers the resolution qPCR cannot.

Learn more: https://www.cd-genomics.com/diseasepanel/pathogens-detection.html

10/08/2026

Hereditary Cancer Panel Sequencing by CD Genomics

Hereditary cancer risk assessment does not always require whole-exome scale. Targeted panels that deeply cover well-characterized predisposition genes can deliver interpretable results more efficiently.

CD Genomics provides a 37-gene hereditary cancer panel using amplicon sequencing. The panel covers genes associated with breast, ovarian, colorectal, prostate, gastric, uterine, and other hereditary cancer syndromes, including BRCA1/2, MLH1, MSH2, MSH6, PMS2, APC, TP53, and others.

Key features:

— Average sequencing depth > 1000× — Detection of SNVs, InDels, and structural variants — Sample input as low as 200 ng gDNA — Compatible with blood, saliva, tissue, and FFPE — Read alignment, variant calling, and annotation included

This service is intended for research applications focused on hereditary cancer predisposition.

Learn more: https://www.cd-genomics.com/diseasepanel/hereditary-cancer-panel-sequencing.html

09/30/2026

Rare variant GWAS can find coding changes with strong effects, but those associations can be confounded in subtle ways.

A 2026 Nature Communications study by Hanson et al. analyzed 306,991 exomes from UK Biobank and showed that principal components alone do not fully remove confounding from population structure, assortative mating, and family-level effects. Within-sibship checks helped distinguish real signals from artifacts.

For anyone running rare variant scans, the takeaway is practical: add family-based or related sensitivity analyses to the standard QC workflow before trusting an association. This step becomes more important as sample sizes grow and rare variant signals get smaller. Replication in independent cohorts is also essential, because confounding can mimic real biological effects.

Read the paper: https://doi.org/10.1038/s41467-026-73776-9

Several mechanisms can confound rare variant associations in GWAS of unrelated individuals. Here, the authors empirically examine these confounding factors and demonstrate important sensitivity analyses to assess the validity of these.

09/30/2026

Replacing fishmeal with plant protein can reduce flesh pigmentation in rainbow trout. A 2025 study shows the gut microbiome plays a key role.

Villasante et al. fed trout diets with 60%, 36%, or 12% fishmeal. The high-plant-protein group showed lower astaxanthin retention, lower cholesterol and bile acid levels, and a microbiota profile linked to poorer pigmentation. The microbiota shift was one of the clearest signals connecting the feed change to the phenotype.

For this study, the authors used 16S/18S/ITS amplicon sequencing provided by CD Genomics to profile intestinal microbiota on the Illumina HiSeq PE250 platform with 300 bp paired-end reads.

The takeaway: feed formulation changes gut microbes, and those microbes affect how the host handles key nutrients. For aquaculture nutrition, that means microbiome analysis belongs in the same workflow as diet design.

Read the paper: https://doi.org/10.3390/ijms262412072

The replacement of fishmeal with plant-based proteins in aquafeeds is key for sustainable aquaculture but may compromise filet pigmentation in rainbow trout (Oncorhynchus mykiss), a quality trait dependent on astaxanthin (Ax) deposition and metabolism. This study aimed to assess the effects of grade...