A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.
Identifieur interne : 000576 ( PubMed/Corpus ); précédent : 000575; suivant : 000577A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.
Auteurs : Sungjoon Park ; Minsu Kim ; Seokjun Seo ; Seungwan Hong ; Kyoohyung Han ; Keewoo Lee ; Jung Hee Cheon ; Sun KimSource :
- BMC genomics [ 1471-2164 ] ; 2019.
English descriptors
- KwdEn :
- MESH :
- methods : Data Mining, Genomics.
- standards : Cloud Computing.
- Algorithms, Computer Security, Humans, Polymorphism, Single Nucleotide.
Abstract
Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNPs are detectable from the tumor. Many hospitals have developed their own panels that include clinically important SNPs. The genome information exchange between the patient and the hospital has become more popular. However, the genome sequence information is innate and irreversible and thus its leakage has serious consequences. Therefore, protecting one's genome information is critical. On the other side, hospitals may need to protect their own panels. There is no known secure SNP panel scheme to protect both.
DOI: 10.1186/s12864-019-5473-z
PubMed: 30967116
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.</title><author><name sortKey="Park, Sungjoon" sort="Park, Sungjoon" uniqKey="Park S" first="Sungjoon" last="Park">Sungjoon Park</name><affiliation><nlm:affiliation>Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Minsu" sort="Kim, Minsu" uniqKey="Kim M" first="Minsu" last="Kim">Minsu Kim</name><affiliation><nlm:affiliation>Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Seo, Seokjun" sort="Seo, Seokjun" uniqKey="Seo S" first="Seokjun" last="Seo">Seokjun Seo</name><affiliation><nlm:affiliation>Hyperconnect Inc, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Hong, Seungwan" sort="Hong, Seungwan" uniqKey="Hong S" first="Seungwan" last="Hong">Seungwan Hong</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Kyoohyung" sort="Han, Kyoohyung" uniqKey="Han K" first="Kyoohyung" last="Han">Kyoohyung Han</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Keewoo" sort="Lee, Keewoo" uniqKey="Lee K" first="Keewoo" last="Lee">Keewoo Lee</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Cheon, Jung Hee" sort="Cheon, Jung Hee" uniqKey="Cheon J" first="Jung Hee" last="Cheon">Jung Hee Cheon</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Sun" sort="Kim, Sun" uniqKey="Kim S" first="Sun" last="Kim">Sun Kim</name><affiliation><nlm:affiliation>Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea. sunkim.bioinfo@snu.ac.kr.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30967116</idno><idno type="pmid">30967116</idno><idno type="doi">10.1186/s12864-019-5473-z</idno><idno type="wicri:Area/PubMed/Corpus">000576</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000576</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.</title><author><name sortKey="Park, Sungjoon" sort="Park, Sungjoon" uniqKey="Park S" first="Sungjoon" last="Park">Sungjoon Park</name><affiliation><nlm:affiliation>Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Minsu" sort="Kim, Minsu" uniqKey="Kim M" first="Minsu" last="Kim">Minsu Kim</name><affiliation><nlm:affiliation>Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Seo, Seokjun" sort="Seo, Seokjun" uniqKey="Seo S" first="Seokjun" last="Seo">Seokjun Seo</name><affiliation><nlm:affiliation>Hyperconnect Inc, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Hong, Seungwan" sort="Hong, Seungwan" uniqKey="Hong S" first="Seungwan" last="Hong">Seungwan Hong</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Han, Kyoohyung" sort="Han, Kyoohyung" uniqKey="Han K" first="Kyoohyung" last="Han">Kyoohyung Han</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Keewoo" sort="Lee, Keewoo" uniqKey="Lee K" first="Keewoo" last="Lee">Keewoo Lee</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Cheon, Jung Hee" sort="Cheon, Jung Hee" uniqKey="Cheon J" first="Jung Hee" last="Cheon">Jung Hee Cheon</name><affiliation><nlm:affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</nlm:affiliation></affiliation></author><author><name sortKey="Kim, Sun" sort="Kim, Sun" uniqKey="Kim S" first="Sun" last="Kim">Sun Kim</name><affiliation><nlm:affiliation>Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea. sunkim.bioinfo@snu.ac.kr.</nlm:affiliation></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Cloud Computing (standards)</term><term>Computer Security</term><term>Data Mining (methods)</term><term>Genomics (methods)</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Data Mining</term><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Cloud Computing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Computer Security</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNPs are detectable from the tumor. Many hospitals have developed their own panels that include clinically important SNPs. The genome information exchange between the patient and the hospital has become more popular. However, the genome sequence information is innate and irreversible and thus its leakage has serious consequences. Therefore, protecting one's genome information is critical. On the other side, hospitals may need to protect their own panels. There is no known secure SNP panel scheme to protect both.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30967116</PMID><DateCompleted><Year>2019</Year><Month>08</Month><Day>28</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>Suppl 2</Issue><PubDate><Year>2019</Year><Month>Apr</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.</ArticleTitle><Pagination><MedlinePgn>188</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-019-5473-z</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNPs are detectable from the tumor. Many hospitals have developed their own panels that include clinically important SNPs. The genome information exchange between the patient and the hospital has become more popular. However, the genome sequence information is innate and irreversible and thus its leakage has serious consequences. Therefore, protecting one's genome information is critical. On the other side, hospitals may need to protect their own panels. There is no known secure SNP panel scheme to protect both.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In this paper, we propose a secure SNP panel scheme using homomorphically encrypted K-mers without requiring SNP calling on the user side and without revealing the panel information to the user. Use of the powerful homomorphic encryption technique is desirable, but there is no known algorithm to efficiently align two homomorphically encrypted sequences. Thus, we designed and implemented a novel secure SNP panel scheme utilizing the computationally feasible equality test on two homomorphically encrypted K-mers. To make the scheme work correctly, in addition to SNPs in the panel, sequence variations at the population level should be addressed. We designed a concept of Point Deviation Tolerance (PDT) level to address the false positives and false negatives. Using the TCGA BRCA dataset, we demonstrated that our scheme works at the level of over a hundred thousand somatic mutations. In addition, we provide a computational guideline for the panel design, including the size of K-mer and the number of SNPs.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The proposed method is the first of its kind to protect both the user's sequence and the hospital's panel information using the powerful homomorphic encryption scheme. We demonstrated that the scheme works with a simulated dataset and the TCGA BRCA dataset. In this study, we have shown only the feasibility of the proposed scheme and much more efforts should be done to make the scheme usable for clinical use.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Sungjoon</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Minsu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Seo</LastName><ForeName>Seokjun</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Hyperconnect Inc, Seoul, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hong</LastName><ForeName>Seungwan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Han</LastName><ForeName>Kyoohyung</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Keewoo</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheon</LastName><ForeName>Jung Hee</ForeName><Initials>JH</Initials><AffiliationInfo><Affiliation>Department of Mathematical Sciences, Seoul National University, Seoul, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Sun</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea. sunkim.bioinfo@snu.ac.kr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. sunkim.bioinfo@snu.ac.kr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea. sunkim.bioinfo@snu.ac.kr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>04</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC 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