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New Nanopore-Based Telomere Profiling Approach Points to Chromosome-Specific Length Variation

NEW YORK – With the help of a newly developed nanopore sequencing method, a team led by investigators at Johns Hopkins University School of Medicine and the University of California, Santa Cruz, has uncovered conserved telomere length differences that coincide with the chromosome end being considered.

"Human health is profoundly affected by telomere length, yet the detailed mechanism of length regulation is poorly understood," senior author Carol Greider, a researcher affiliated with Johns Hopkins and the UCSC, and her colleagues wrote in Science on Thursday.

For example, prematurely shortened telomeres have been linked to age-related degenerative disease, while unusually long telomeres have been implicated in cancer, the team explained, noting that a "lack of widely accessible and accurate methods for measuring telomere length has limited development of targeted therapies."

With that in mind, the investigators came up with a nanopore sequencing strategy dubbed "Telomere Profiling" for spelling out telomere lengths in relation to other parts of the genome. The method combines bioinformatics with biotinylated oligonucleotide telomere end tagging, sample multiplexing, and long read sequencing on the Oxford Nanopore Technology MinIon platform.

The approach was validated in cohort blood and cell line samples, the researchers wrote, and through analyses on individuals with clinical conditions known to abbreviate telomere lengths, such as idiopathic pulmonary fibrosis. In the latter analyses, the Telomere Profiling results broadly tracked with those found using a clinical FlowFISH assay.

"Telomere Profiling makes precision investigation of telomere length widely accessible for laboratory, clinical, and drug discovery efforts and will allow deeper insights into telomere biology," the authors explained, noting that the price tag for multiplexed Telomere Profiling comes in at around $80 to $140 per sample.

In an initial analysis on blood or peripheral blood mononuclear cells (PBMC) from half a dozen individuals between infancy and the age of 91 years, the team saw consistent variation in telomere lengths that were specific to the chromosome being considered — patterns that were backed up by subsequent Southern blot analyses and confirmed with Telomere Profiling on PBMC samples from 11 more individuals between infancy and 84 years.

The team also found chromosome end-related telomere length differences when they used the Telomere Profiling approach to profile length distribution patterns across a population of 132 individuals who were between zero and 90 years old, replicating those differences in a newborn blood sample and a diploid human cell line.

In particular, the team tracked down longer-than-usual telomeres on the ends of specific chromosome 4, 12, and 3 arms and shorter telomeres on chromosome 17, 20, and 12 arms in the newborn blood sample.

"The same rank order was found in newborn cord blood," the authors reported, "suggesting that telomere length is determined at birth and chromosome end-specific telomere length differences are maintained as telomeres shorten with age."

"We did not prospectively choose our samples to be representative of the diversity of the human population, but rather to span a wide age range," the authors noted. "However, future studies should be powered to examine whether certain chromosome ends are consistently the shortest or longest more broadly in a diverse human population."