Methodological development of human telomere sequencing with the Oxford Nanopore Technologies

Abstract: Human DNA is protected with telomeres, which consist of the repetitive DNA-sequence TTAGGG. A 3’-overhang folds back and in combination with the shelterin complex protects the ends of the DNA. Telomeres shorten over time due to the end replication problem in cell proliferation which eventually leads to senescence or apoptosis, making the telomeres an ageing indicator. Some individuals are born with defected telomerase and/or defected shelterin, called telomere biology disorders (TBD), and develop illness in their adulthood due to the defects causing shorter telomeres. Cancer cells have found mechanisms to avoid cell death due to too short telomeres, 85-90% of all cancers use telomerase to maintain telomere length while about 15-10% of all cancers have developed an alternative lengthening of telomeres (ALT)-pathway to ensure cell proliferation and avoid apoptosis by developing abnormal long telomeres. Measuring telomere length is of interest but has been proven difficult to do by sequencing due to their repetitive motif. With third-generation sequencing (TGS), which is long-read sequencing, telomeres can be sequenced, providing telomere length analysis with a nucleotide resolution. The aim for this study was to develop a method using the TGS platform from Oxford Nanopore Technologies (ONT) to sequence human telomeres for telomere length analysis. Samples used were healthy blood donors’ DNA from whole blood, unfragmented and of high concentration. Different oligonucleotides were tested to find an approach which gave double stranded DNA with blunt ends, needed for sequencing. During the process a need to enrich for telomeres arose and tests were performed to find a method where that could be achieved. Some enrichment was found but of unclear quality and further tests need to be performed to further settle in a method for sequencing of human telomeres using ONT.