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Diagnostics Genetics and epigenetics, Biochemistry and molecular biology, Digital and computational pathology

The Genomic Jotter

Causes and Consequences
 

A genome-wide analysis of individuals with clonal hematopoiesis (CH) has increased the number of germline associations with CH in European-ancestry populations from four to 14 and revealed key insights into the heterogeneity of these associations (1). An increased risk of a range of conditions was also found in individuals with CH.

Digging Deeper
 

A genome-wide association study of group B Streptococcus has identified variations in the bacteria that may be linked with disease onset time and invasion of the central nervous system (2) – highlighting the need to integrate microbial population genomics into clinical pathogen surveillance.

Wide Awake
 

Over 200 loci have been associated with insomnia, but how many more are yet to be discovered? A new study has identified 554 risk loci, including 364 novel loci, and suggests a strategy for prioritizing genes (3). The approach enabled researchers to establish specific hypotheses about the disorder that may have been missed using traditional methods.

The Rest Was History
 

Trichuris trichiura is a human-infective whipworm responsible for the neglected tropical disease trichuriasis. Using modern genome data and ancient samples from human and non-human primates, researchers have conducted the first population genomics study of T. trichiura (4). With samples spanning multiple continents, the results provide insight into zoonotic reservoirs of human-infective T. trichiura and establish a genetic framework for its genomic epidemiology.

Urgent Attention Required
 

Without proper diagnosis, genetic disorders in infants can progress rapidly and lead to severe morbidity or mortality if not treated immediately. To help overcome this, researchers have developed Genome-to-Treatment – an automated virtual system for diagnosing genetic conditions and informing acute treatment (5). The system achieves a diagnosis in 13.5 hours by expedited whole-genome sequencing and could help lead to better outcomes in children with genetic disorders requiring urgent care.

Flex with plexDIA
 

Researchers have developed a computational framework to increase throughput of sensitive proteomics. Named “plexDIA,” the framework improves throughput in accordance with the number of labels without reducing accuracy or proteome coverage (6). In single human cells, the framework was able to quantify about 1,000 proteins per cell.

Star Struck
 

Using a computational algorithm known as “Starfish,” researchers have identified six complex genomic rearrangement signatures in cancers from their copy number and breakpoint patterns (7).  Benchmarking efforts revealed the signatures to be highly accurate and biologically meaningful. Three signatures had not been reported previously, including a unique signature the researchers called “hourglass chromothripsis” that is abundant in prostate cancer. The researchers highlighted that this signature is associated with mutant SPOP and may be linked to genome instability.

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  1. SP Kar et al., Nat Genet, [Online ahead of print] (2022). PMID: 35835912.
  2. C Chaguza et al., Nat Commun, 13, 4215 (2022). PMID: 35864107.
  3. K Watanabe et al., Nat Genet, [Online ahead of print] (2022). PMID: 35835914.
  4. SR Doyle et al., Nat Commun, 13, 3888 (2022). PMID: 35794092.
  5. MJ Owen et al., Nat Commun, 13, 4057 (2022). PMID: 35882841.
  6. J Derks et al., Biotechnol, [Online ahead of print] (2022). PMID: 35835881.
  7. L Bao et al., Nat Cancer, [Online ahead of print] (2022). PMID: 35835961.
About the Author
Liv Gaskill

During my undergraduate degree in psychology and Master’s in neuroimaging for clinical and cognitive neuroscience, I realized the tasks my classmates found tedious – writing essays, editing, proofreading – were the ones that gave me the greatest satisfaction. I quickly gathered that rambling on about science in the bar wasn’t exactly riveting for my non-scientist friends, so my thoughts turned to a career in science writing. At Texere, I get to craft science into stories, interact with international experts, and engage with readers who love science just as much as I do.

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