Search bioRxivSearch

Biology subjects

Speyer, D.

Publications and source records attributed to Speyer, D..

2 recordsLinked to original sources

DNA.Land: A Digital Biobank Using A Massive Crowdsourcing Approach

Precision medicine necessitates large scale collections of genomes and phenomes. Despite decreases in the costs of genomic technologies, collecting these types of information at scale is still a daunting task that poses logistical challenges and requires consortium-scale resources. Here, we describe DNA.Land, a digital biobank to collect genome and phenomes with a fraction of the resources of traditional studies at the same scale. Our approach relies on crowd-sourcing data from the rapidly growing number of individuals that have access to their own genomic datasets through Direct-to-Consumer (DTC) companies. To recruit participants, we developed a series of automatic return-of-results features in DNA.Land that increase users engagement while stratifying human subject research protection. So far, DNA.Land has collected over 43,000 genomes in 20 months of operation, orders of magnitude higher than previous digital attempts by academic groups. We report lessons learned in running a digital biobank, our technical framework, and our approach regarding ethical, legal, and social implications.

bioinformatics

Rapid DNA Re-Identification for Cell Line Authentication and Forensics

DNA re-identification is used for a broad range of applications, ranging from cell line authentication to crime scene sample identification. However, current re-identification schemes suffer from high latency. Here, we describe a rapid, inexpensive, and portable strategy to re-identify human DNA called MinION sketching. Using data from Oxford Nanopore Technologies sequencer, MinION sketching requires only 3min of sequencing and [~]91 random SNPs to identify a sample, enabling near real-time applications of DNA re-identification. This method capitalizes on the vastly growing availability of genomic reference data for individuals and cancer cell lines. Hands-on preparation of the samples can be reduced to <1 hour. This empowers the application of MinION sketching in research settings for routine cell line authentication or in forensics.\n\nSoftware is available at https://github.com/TeamErlich/personal-identification-pipeline

cell biology