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Analytical Approach Applied to Repeat-Rich, Clinically Relevant Pangenome Sequences

In a paper appearing in Nature Methods, a team from GeneDX, the Foundation of Biological Data Science, Baylor College of Medicine, and elsewhere presents a software package known as the PanGenome Research Tool Kit (PGR-TK) that is designed to uncover small-to-large forms of genetic variation in human genome assemblies. Along with analyses of the class II major histocompatibility complex, for example, the researchers used PGR-TK tools to dig into infertility- and eye disease-related regions on the Y chromosome and X chromosome, respectively, before applying the approach to Human Pangenome Reference Consortium sequence data spanning nearly 400 repeat-rich, medically relevant genes originally found in the Genome in a Bottle (GIAB) dataset. "Our initial analysis of the GIAB clinical and medically important genes … with a pangenome graph approach will help the research community to adapt the pangenome resource for clinical and medical genetic applications," the authors report. "Tools for visualizing and analyzing complicated rearrangement loci such as PGR-TK will be essential for better variant calling and understanding how structural variations with repeats affect the results for the community."

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.