Abstract 322: Ultraplex genome and exome sequencing of rare single cells
Abstract Single-cell genome analysis enables researchers to gain novel insights into tumor heterogeneity. Conducting single-cell genomic analysis using next-generation sequencing (NGS) methods has traditionally been challenging since the amount of genomic DNA present in a single cell is limited. PCR...
Saved in:
Published in | Cancer research (Chicago, Ill.) Vol. 84; no. 6_Supplement; p. 322 |
---|---|
Main Authors | , , , , , |
Format | Journal Article |
Language | English |
Published |
22.03.2024
|
Online Access | Get full text |
Cover
Loading…
Abstract | Abstract
Single-cell genome analysis enables researchers to gain novel insights into tumor heterogeneity. Conducting single-cell genomic analysis using next-generation sequencing (NGS) methods has traditionally been challenging since the amount of genomic DNA present in a single cell is limited. PCR-based amplification methods normally have high error rates, low coverage uniformity, and extensive allelic drop-outs making interpretation of SNVs and CNVs challenging.Here we introduce a new whole-genome amplification method which utilizes an optimized isothermal DNA amplification reaction with a Hi-fidelity, error correcting polymerase and downstream library preparation protocol to allow pooling of amplified DNA. The key DNA amplification steps use multiple displacement amplification (MDA) technology to amplify gDNA directly from single cells, nuclei or previously isolated genomic DNA. During the MDA reaction, sample-barcodes are incorporated into the newly synthetized DNA, allowing the amplified DNA to be pooled and processed in to one ultraplex library. This method saves library preparation time, reduces DNA library costs and limits plastic consumable usage.Our current workflow allows 24 samples to be multiplexed in one library and 24 libraries to be produced for a total of 576 samples per sequencing flow cell. This method can be used to investigate chromosomal instability with low pass sequencing or SNV and CNV analysis following whole genome, exome-capture workflows.
Citation Format: Ioanna Andreou, Samuel Rulli, Katja Heitz, Silke Huebner, Christin Meerschiff, Eric Lader. Ultraplex genome and exome sequencing of rare single cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 322. |
---|---|
AbstractList | Abstract
Single-cell genome analysis enables researchers to gain novel insights into tumor heterogeneity. Conducting single-cell genomic analysis using next-generation sequencing (NGS) methods has traditionally been challenging since the amount of genomic DNA present in a single cell is limited. PCR-based amplification methods normally have high error rates, low coverage uniformity, and extensive allelic drop-outs making interpretation of SNVs and CNVs challenging.Here we introduce a new whole-genome amplification method which utilizes an optimized isothermal DNA amplification reaction with a Hi-fidelity, error correcting polymerase and downstream library preparation protocol to allow pooling of amplified DNA. The key DNA amplification steps use multiple displacement amplification (MDA) technology to amplify gDNA directly from single cells, nuclei or previously isolated genomic DNA. During the MDA reaction, sample-barcodes are incorporated into the newly synthetized DNA, allowing the amplified DNA to be pooled and processed in to one ultraplex library. This method saves library preparation time, reduces DNA library costs and limits plastic consumable usage.Our current workflow allows 24 samples to be multiplexed in one library and 24 libraries to be produced for a total of 576 samples per sequencing flow cell. This method can be used to investigate chromosomal instability with low pass sequencing or SNV and CNV analysis following whole genome, exome-capture workflows.
Citation Format: Ioanna Andreou, Samuel Rulli, Katja Heitz, Silke Huebner, Christin Meerschiff, Eric Lader. Ultraplex genome and exome sequencing of rare single cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 322. |
Author | Heitz, Katja Huebner, Silke Andreou, Ioanna Lader, Eric Meerschiff, Christin Rulli, Samuel |
Author_xml | – sequence: 1 givenname: Ioanna surname: Andreou fullname: Andreou, Ioanna – sequence: 2 givenname: Samuel surname: Rulli fullname: Rulli, Samuel – sequence: 3 givenname: Katja surname: Heitz fullname: Heitz, Katja – sequence: 4 givenname: Silke surname: Huebner fullname: Huebner, Silke – sequence: 5 givenname: Christin surname: Meerschiff fullname: Meerschiff, Christin – sequence: 6 givenname: Eric surname: Lader fullname: Lader, Eric |
BookMark | eNqdjkELgjAcxUcYpNU36LAvoG3TkXSTKLx0q_NY9leMOW0zsG_fpIjOnd57P3jwC5CnWw0IrSiJKOXpmvI4DTdJwqPsyAhLwpixCfK_2PvpMxRYeyOEcEq4j_LsYnsjix67zxaflRudggFXoNsGsNRXDMPYLNwfoItaV7gtsZHGITcU4AKUsgs0LaWysPzkHCWH_WmXh4VprTVQis7UjTRPQYkYrcWoJEYl8bYWziD-8_YCwzpMOw |
ContentType | Journal Article |
DBID | AAYXX CITATION |
DOI | 10.1158/1538-7445.AM2024-322 |
DatabaseName | CrossRef |
DatabaseTitle | CrossRef |
DatabaseTitleList | CrossRef |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Medicine |
EISSN | 1538-7445 |
EndPage | 322 |
ExternalDocumentID | 10_1158_1538_7445_AM2024_322 |
GroupedDBID | --- -ET 18M 29B 34G 39C 476 53G 5GY 5RE 6J9 AAJMC AAYXX ABOCM ACGFO ACIWK ACPRK ADBBV ADNWM AENEX AFHIN AFOSN AFRAH ALMA_UNASSIGNED_HOLDINGS BAWUL BTFSW CITATION CS3 DIK DU5 EBS EJD F5P FRP GX1 IH2 KQ8 L7B LSO OK1 P0W P2P PQQKQ RCR RHF RHI RNS SJN TR2 W2D WH7 WOQ YKV YZZ |
ID | FETCH-crossref_primary_10_1158_1538_7445_AM2024_3223 |
ISSN | 1538-7445 |
IngestDate | Thu Sep 26 19:41:37 EDT 2024 |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 6_Supplement |
Language | English |
LinkModel | OpenURL |
MergedId | FETCHMERGED-crossref_primary_10_1158_1538_7445_AM2024_3223 |
ParticipantIDs | crossref_primary_10_1158_1538_7445_AM2024_322 |
PublicationCentury | 2000 |
PublicationDate | 2024-03-22 |
PublicationDateYYYYMMDD | 2024-03-22 |
PublicationDate_xml | – month: 03 year: 2024 text: 2024-03-22 day: 22 |
PublicationDecade | 2020 |
PublicationTitle | Cancer research (Chicago, Ill.) |
PublicationYear | 2024 |
SSID | ssj0005105 |
Score | 4.5865088 |
Snippet | Abstract
Single-cell genome analysis enables researchers to gain novel insights into tumor heterogeneity. Conducting single-cell genomic analysis using... |
SourceID | crossref |
SourceType | Aggregation Database |
StartPage | 322 |
Title | Abstract 322: Ultraplex genome and exome sequencing of rare single cells |
Volume | 84 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3dS8MwEA9zgvgifuI3efBttLo26VrfxlCGMkHZYG8laTP86NoxNxj-J_635pKsrXOI86W0aXtNuV-vucsvdwhdMC4o9X3PanhMOihsQKzgivpWHBMycOKAcjWj23nw2j1y16f9SuWzxFqaTrgdfSxdV_Ifrco2qVdYJbuCZnOhskHuS_3KrdSw3P5Jx00OgYpoUpPfC7j2vUQejhIxg8LI2VDPDIgZ7BnKtOE4j4HvBVGCRNQgdP9eHqO2AAjjmkkD9KzmeTVhQxmUJLG_hQ_iscim6kzG0jS38k8wy6RjzsOpyHkcbfGiKsgCjeOVFaASfF4C7CV5E-VYhEOAjOU4C-azQXSCSFssaTM2V5eFM9jyQlXBtKD6aFvqGsmifPTT4lNYxZA_xG52VMfym8sJthd-fDkdUTlC1A9BSghSQi0llFLW0LrTCCj49fePRSJ6qtmx-XPNqkwp5XJZX0qjntLwpbuNtozfgZsaRDuoItJdtNExzIo91J5jCUs51zhHEtZIwhJJWCEJF0jC2QADkrBGElZI2kfk9qbbalvznoQjndAk_O393QNUTbNUHCLsMofGdZ97jLiEU8ZdEdQFocwjURRReoRWE3284vUnaLMA3SmqTsZTcSaHhBN-rpTzBcD9W9E |
link.rule.ids | 315,786,790,27957,27958 |
linkProvider | Colorado Alliance of Research Libraries |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Abstract+322%3A+Ultraplex+genome+and+exome+sequencing+of+rare+single+cells&rft.jtitle=Cancer+research+%28Chicago%2C+Ill.%29&rft.au=Andreou%2C+Ioanna&rft.au=Rulli%2C+Samuel&rft.au=Heitz%2C+Katja&rft.au=Huebner%2C+Silke&rft.date=2024-03-22&rft.issn=1538-7445&rft.eissn=1538-7445&rft.volume=84&rft.issue=6_Supplement&rft.spage=322&rft.epage=322&rft_id=info:doi/10.1158%2F1538-7445.AM2024-322&rft.externalDBID=n%2Fa&rft.externalDocID=10_1158_1538_7445_AM2024_322 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1538-7445&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1538-7445&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1538-7445&client=summon |