Main menu

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing


Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-based methods.

Here we introduce a CRISPR–Cas-based enrichment strategy for nanopore sequencing combined with an algorithm for raw signal analysis. Our method, termed STRique for short tandem repeat identification, quantification and evaluation, integrates conventional sequence mapping of nanopore reads with raw signal alignment for the localization of repeat boundaries and a hidden Markov model-based repeat counting mechanism.

We demonstrate the precise quantification of repeat numbers in conjunction with the determination of CpG methylation states in the repeat expansion and in adjacent regions at the single-molecule level without amplification.

Our method enables the study of previously inaccessible genomic regions and their epigenetic marks.

Authors: Pay Giesselmann, Björn Brändl, Etienne Raimondeau, Rebecca Bowen, Christian Rohrandt, Rashmi Tandon, Helene Kretzmer, Günter Assum, Christina Galonska, Reiner Siebert, Ole Ammerpohl, Andrew Heron, Susanne A. Schneider, Julia Ladewig, Philipp Koch, Bernhard M. Schuldt, James E. Graham, Alexander Meissner, Franz-Josef Müller

入門

MinION Starter Packを購入 ナノポア製品の販売 シークエンスサービスプロバイダー グローバルディストリビューター

お問い合わせ

Intellectual property Cookie policy Corporate reporting Privacy policy Terms & conditions Accessibility

Oxford Nanoporeについて

Contact us 経営陣 メディアリソース & お問い合わせ先 投資家向け Oxford Nanopore社で働く BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Japanese flag