Exploiting Index Cross-Talk to Modify Variant Calls

Abstract

Modern next-generation DNA sequencers support multiplex sequencing to improve throughput and decrease costs. This is done by pooling and sequencing samples together in parallel, which are later demultiplexed according to their unique indexes 1, 2 . When reads are assigned to the wrong index, called index cross-talk, information is leaked between samples 3-6 . This creates a physical information side-channel, a well known class of vulnerabilities in information security [7][8][9][10] , that may be used to modify downstream results. Here we demonstrate the feasibility of such an attack through the use of a separately indexed library that causes a wild-type human exome to be misclassified as heterozygous at the sickle-cell locus. Simple methods can be used to minimize or detect attempts to modify genetic variants using this side-channel, such as filtering by read quality or finding outliers in read coverage. To further minimize this risk we recommend the use of new library preparation methods that reduce index cross-talk, like unique dual indexes 11,12 , whenever samples are sequenced together in important applications. Biotechnology that interfaces molecular and digital information, like DNA sequencers, may have security risks typically associated with information systems, including the side-channel vulnerability described in this study. We encourage the community to consider the security of genomics-information pipelines before they reach mass adoption.

A Systematic Review of the Criminogenic Potential of Synthetic Biology and Routes to Future Crime Prevention

“…This increasing integration and dependence on the digital space (for example, computer-controlled instruments within biomanufacturing processes) creates a new category of risks between cyber and biological systems. Cyber-biocrime describes criminal activities carried out by combined means of computers/Internet and biological/biochemical material, and was discussed in six studies (Ney et al, 2017 , 2018 ; Wintle et al, 2017 ; Peccoud et al, 2018 ; Faezi et al, 2019 ; Qu, 2019 ). Peccoud et al introduce the need for “cyberbiosecurity” to prevent (for example) the manufacture of nefarious products through the tampering of electronic orders of DNA sequences or the interception of shipments.…”

“…Ney et al ( 2018 ) demonstrated targeted “mis-genotyping,” where a healthy DNA sample may be misclassified as one (in their example) with anemia ( Figure 5 , Table 2 , Supplementary Table 1 ). This was achieved by a physical side channel attack on modern next-generation DNA sequencers (NGS) that are capable of sequencing multiple sequences at once to increase throughput.…”

“…Regulation and accelerated funds within defense research were some of the issues discussed in relation to government. Apropos industry, discussion included the increasing numbers of commercial service providers (Hsu and Sandford, 2007 ; Turnbaugh et al, 2007 ; Ali et al, 2016 ; Murch et al, 2018 ; Ney et al, 2018 ; Lewis, 2019 ) who prioritize profit, possibly at the expense of security. This is exemplified in the case of the IoT (DDCMS, 2018 ; Blythe and Johnson, 2019 ) and is expected to extend to biotech start-ups.…”

Facing the 2020 pandemic: What does cyberbiosecurity want us to know to safeguard the future?

“…Due to the increased reliance of the bioscience fields on cyberphysical systems (CPS, Fig. 3 below), potentials for exploitation exist at each point where bioengineered or biomanufactured processes or services interface with the cyber and the physical domain, whereby attackers may exploit unsecured networks and remotely manipulate biologic data, exploit biologic agents, or affect physical processing involving biological materials, that result (whether intentionally or unintentionally) in unwanted or dangerous biological outcomes [ [4] , [5] , [6] , [7] ].

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