Human telomere length is chromosome specific and conserved across individuals.

Short telomeres cause age-related disease and long telomeres predispose to cancer; however, the mechanisms regulating telomere length are unclear. Current methods for telomere length measurement are not direct, precise, or widely accessible. Here we describe a direct nanopore telomere profiling assay using an Oxford Nanopore Technology (ONT) MinION that is easy to implement, precise, and cost effective with broad applications in research, and the clinic. Telomere length measurement is currently used in clinical settings to make highly consequential treatment decisions. Using patient samples our method returned similar results to the clinical, FlowFISH assay. Telomere profiling enables mapping of the telomere to specific chromosomes, and we identified both chromosome-specific and haplotype-specific telomere length distribution with a remarkable 6kb difference between some telomere lengths. Further, we found that specific chromosome ends were consistently shorter or longer than the average length across 150 individuals. The presence of conserved chromosome end-specific telomere lengths suggests there are new paradigms in telomere biology that are yet to be explored. Understanding these mechanisms will allow deeper insights into telomere biology that can lead to new approaches to disease.