Additional file 1: Figure S1. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Accurate Mutation Detection in Cancer Through Improved Error Suppression and Quantification of Molecular Complexity

Wang, Ting Ting

June 2018

DNA from cancer cells is often masked by nucleic acids from normal cells in tumour tissues and blood...

Overview of the Duplex Sequencing methodology.

Scott R. Kennedy (463286)
Jesse J. Salk (319884)
Michael W. Schmitt (463287)
Lawrence A. Loeb (335078)

September 2013

<p>(A) Adapter design with random double-stranded tag sequence and invariant spacer sequence. (B) Li...

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

James L. O’Donnell (3181911)
Ryan P. Kelly (255075)
Natalie C. Lowell (3181914)
Jesse A. Port (124035)

March 2016

<div><p>Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversi...

Additional file 3: Figure S3. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Laura MacConaill (145626)
Robert Burns (1728919)
Anwesha Nag (3264552)
Haley Coleman (4745277)
Michael Slevin (4745286)
Kristina Giorda (4745280)
Madelyn Light (4745292)
Kevin Lai (26571)
Mirna Jarosz (4745283)
Matthew McNeill (2882684)
Matthew Ducar (3564323)
Matthew Meyerson (24538)
Aaron Thorner (4745289)

January 2018

Schematic of the sources of sample cross-talk including adapter contamination, index hopping during ...

Additional file 6: Figure S6. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Laura MacConaill (145626)
Robert Burns (1728919)
Anwesha Nag (3264552)
Haley Coleman (4745277)
Michael Slevin (4745286)
Kristina Giorda (4745280)
Madelyn Light (4745292)
Kevin Lai (26571)
Mirna Jarosz (4745283)
Matthew McNeill (2882684)
Matthew Ducar (3564323)
Matthew Meyerson (24538)
Aaron Thorner (4745289)

January 2018

Schematic of the experiment used to measure adapter contamination and multiplexed capture index hopp...

Additional file 5: Figure S5. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Laura MacConaill (145626)
Robert Burns (1728919)
Anwesha Nag (3264552)
Haley Coleman (4745277)
Michael Slevin (4745286)
Kristina Giorda (4745280)
Madelyn Light (4745292)
Kevin Lai (26571)
Mirna Jarosz (4745283)
Matthew McNeill (2882684)
Matthew Ducar (3564323)
Matthew Meyerson (24538)
Aaron Thorner (4745289)

January 2018

Level of cross-talk using unique, dual-matched indexed adapters on Illumina HiSeq 2500. The 96-well ...

Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

MacConaill, Laura E.
Burns, Robert T.
Nag, Anwesha
Coleman, Haley A.
Slevin, Michael K.
Giorda, Kristina
Light, Madelyn
Lai, Kevin
Jarosz, Mirna
McNeill, Matthew S.
Ducar, Matthew D.
Meyerson, Matthew
Thorner, Aaron R.

February 2018

Background: Sample index cross-talk can result in false positive calls when massively parallel seque...

Additional file 7: of Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier

Jongsuk Chung (6468518)
Ki-Wook Lee (6468521)
Chung Lee (203278)
Seung-Ho Shin (791971)
Sungkyu Kyung (6468524)
Hyo-Jeong Jeon (4265824)
Sook-Young Kim (189650)
Eunjung Cho (6468527)
Chang Yoo (3436814)
Dae-Soon Son (4265827)
Woong-Yang Park (207980)
Donghyun Park (1820776)

March 2019

Sequencing metrics depending on input DNA amounts. Sequencing metrics were obtained without UMIs, wi...

Additional file 6: of Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier

Jongsuk Chung (6468518)
Ki-Wook Lee (6468521)
Chung Lee (203278)
Seung-Ho Shin (791971)
Sungkyu Kyung (6468524)
Hyo-Jeong Jeon (4265824)
Sook-Young Kim (189650)
Eunjung Cho (6468527)
Chang Yoo (3436814)
Dae-Soon Son (4265827)
Woong-Yang Park (207980)
Donghyun Park (1820776)

March 2019

Analysis of UMI errors. (a) The frequency of reads tagged with erroneous UMIs was estimated by UMI-t...

Additional file 3: of Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Maura Costello (5185436)
Mark Fleharty (5185445)
Justin Abreu (5185424)
Yossi Farjoun (3521399)
Steven Ferriera (272769)
Laurie Holmes (5185418)
Brian Granger (4863007)
Lisa Green (2470498)
Tom Howd (5185448)
Tamara Mason (5185421)
Gina Vicente (5185430)
Michael Dasilva (5185427)
Wendy Brodeur (169844)
Timothy DeSmet (5185433)
Sheila Dodge (5185442)
Niall Lennon (5185439)
Stacey Gabriel (274305)

May 2018

Suggested guidelines for designing robust indexes for Illumina sequencing. (DOCX 129Â kb

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

Glenn, Travis C
Nilsen, Roger A
Kieran, Troy J
Sanders, Jon G
Bayona-Vásquez, Natalia J
Finger, John W
Pierson, Todd W
Bentley, Kerin E

January 2019

Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (...

Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity

Staadig, Adam
Hedman, Johannes
Tillmar, Andreas

January 2023

One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. ...

Data from: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies

O'Donnell, James L.
Kelly, Ryan P.
Port, Jesse A.
Lowell, Natalie C.

March 2016

Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at al...

Additional file 1: of Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform

Qiaoling Li (290816)
Xia Zhao (215170)
Wenwei Zhang (165134)
Lin Wang (11986)
Jingjing Wang (140791)
Dongyang Xu (303547)
Zhiying Mei (6457478)
Qiang Liu (166143)
Shiyi Du (6457481)
Zhanqing Li (6457484)
Xinming Liang (3292728)
Xiaman Wang (6457487)
Hanmin Wei (6457490)
Pengjuan Liu (6457493)
Jing Zou (550318)
Hanjie Shen (301956)
Ao Chen (3465824)
Snezana Drmanac (3465818)
Jia Liu (41593)
Li Li (14993)
Hui Jiang (102809)
Yongwei Zhang (2333089)
Jian Wang (5901)
Huanming Yang (5905)
Xun Xu (276108)
Radoje Drmanac (3465833)
Yuan Jiang (296541)

March 2019

Table S1. PCR primer sequences for 8 genes. Table S2. Mis-assignment rate of control group with Q30 ...

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing

Tu, N-D
Pope, BJ
Hammet, F
Mahmoodi, M
Tsimiklis, H
Southey, MC
Park, DJ

November 2013

The fulltext of this publication will be made publicly available after relevant embargo periods have...

Accurate Mutation Detection in Cancer Through Improved Error Suppression and Quantification of Molecular Complexity

Wang, Ting Ting

June 2018

DNA from cancer cells is often masked by nucleic acids from normal cells in tumour tissues and blood...

Overview of the Duplex Sequencing methodology.

Scott R. Kennedy (463286)
Jesse J. Salk (319884)
Michael W. Schmitt (463287)
Lawrence A. Loeb (335078)

September 2013

<p>(A) Adapter design with random double-stranded tag sequence and invariant spacer sequence. (B) Li...

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

James L. O’Donnell (3181911)
Ryan P. Kelly (255075)
Natalie C. Lowell (3181914)
Jesse A. Port (124035)

March 2016

<div><p>Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversi...

Additional file 3: Figure S3. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Laura MacConaill (145626)
Robert Burns (1728919)
Anwesha Nag (3264552)
Haley Coleman (4745277)
Michael Slevin (4745286)
Kristina Giorda (4745280)
Madelyn Light (4745292)
Kevin Lai (26571)
Mirna Jarosz (4745283)
Matthew McNeill (2882684)
Matthew Ducar (3564323)
Matthew Meyerson (24538)
Aaron Thorner (4745289)

January 2018

Schematic of the sources of sample cross-talk including adapter contamination, index hopping during ...

Additional file 6: Figure S6. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Laura MacConaill (145626)
Robert Burns (1728919)
Anwesha Nag (3264552)
Haley Coleman (4745277)
Michael Slevin (4745286)
Kristina Giorda (4745280)
Madelyn Light (4745292)
Kevin Lai (26571)
Mirna Jarosz (4745283)
Matthew McNeill (2882684)
Matthew Ducar (3564323)
Matthew Meyerson (24538)
Aaron Thorner (4745289)

January 2018

Schematic of the experiment used to measure adapter contamination and multiplexed capture index hopp...

Additional file 5: Figure S5. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Laura MacConaill (145626)
Robert Burns (1728919)
Anwesha Nag (3264552)
Haley Coleman (4745277)
Michael Slevin (4745286)
Kristina Giorda (4745280)
Madelyn Light (4745292)
Kevin Lai (26571)
Mirna Jarosz (4745283)
Matthew McNeill (2882684)
Matthew Ducar (3564323)
Matthew Meyerson (24538)
Aaron Thorner (4745289)

January 2018

Level of cross-talk using unique, dual-matched indexed adapters on Illumina HiSeq 2500. The 96-well ...

Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

MacConaill, Laura E.
Burns, Robert T.
Nag, Anwesha
Coleman, Haley A.
Slevin, Michael K.
Giorda, Kristina
Light, Madelyn
Lai, Kevin
Jarosz, Mirna
McNeill, Matthew S.
Ducar, Matthew D.
Meyerson, Matthew
Thorner, Aaron R.

February 2018

Background: Sample index cross-talk can result in false positive calls when massively parallel seque...

Additional file 7: of Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier

Jongsuk Chung (6468518)
Ki-Wook Lee (6468521)
Chung Lee (203278)
Seung-Ho Shin (791971)
Sungkyu Kyung (6468524)
Hyo-Jeong Jeon (4265824)
Sook-Young Kim (189650)
Eunjung Cho (6468527)
Chang Yoo (3436814)
Dae-Soon Son (4265827)
Woong-Yang Park (207980)
Donghyun Park (1820776)

March 2019

Sequencing metrics depending on input DNA amounts. Sequencing metrics were obtained without UMIs, wi...

Additional file 6: of Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier

Jongsuk Chung (6468518)
Ki-Wook Lee (6468521)
Chung Lee (203278)
Seung-Ho Shin (791971)
Sungkyu Kyung (6468524)
Hyo-Jeong Jeon (4265824)
Sook-Young Kim (189650)
Eunjung Cho (6468527)
Chang Yoo (3436814)
Dae-Soon Son (4265827)
Woong-Yang Park (207980)
Donghyun Park (1820776)

March 2019

Analysis of UMI errors. (a) The frequency of reads tagged with erroneous UMIs was estimated by UMI-t...

Additional file 3: of Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Maura Costello (5185436)
Mark Fleharty (5185445)
Justin Abreu (5185424)
Yossi Farjoun (3521399)
Steven Ferriera (272769)
Laurie Holmes (5185418)
Brian Granger (4863007)
Lisa Green (2470498)
Tom Howd (5185448)
Tamara Mason (5185421)
Gina Vicente (5185430)
Michael Dasilva (5185427)
Wendy Brodeur (169844)
Timothy DeSmet (5185433)
Sheila Dodge (5185442)
Niall Lennon (5185439)
Stacey Gabriel (274305)

May 2018

Suggested guidelines for designing robust indexes for Illumina sequencing. (DOCX 129Â kb

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

Glenn, Travis C
Nilsen, Roger A
Kieran, Troy J
Sanders, Jon G
Bayona-Vásquez, Natalia J
Finger, John W
Pierson, Todd W
Bentley, Kerin E

January 2019

Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (...

Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity

Staadig, Adam
Hedman, Johannes
Tillmar, Andreas

January 2023

One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. ...

Data from: Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies

O'Donnell, James L.
Kelly, Ryan P.
Port, Jesse A.
Lowell, Natalie C.

March 2016

Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at al...

Additional file 1: of Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform

Qiaoling Li (290816)
Xia Zhao (215170)
Wenwei Zhang (165134)
Lin Wang (11986)
Jingjing Wang (140791)
Dongyang Xu (303547)
Zhiying Mei (6457478)
Qiang Liu (166143)
Shiyi Du (6457481)
Zhanqing Li (6457484)
Xinming Liang (3292728)
Xiaman Wang (6457487)
Hanmin Wei (6457490)
Pengjuan Liu (6457493)
Jing Zou (550318)
Hanjie Shen (301956)
Ao Chen (3465824)
Snezana Drmanac (3465818)
Jia Liu (41593)
Li Li (14993)
Hui Jiang (102809)
Yongwei Zhang (2333089)
Jian Wang (5901)
Huanming Yang (5905)
Xun Xu (276108)
Radoje Drmanac (3465833)
Yuan Jiang (296541)

March 2019

Table S1. PCR primer sequences for 8 genes. Table S2. Mis-assignment rate of control group with Q30 ...

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing

Tu, N-D
Pope, BJ
Hammet, F
Mahmoodi, M
Tsimiklis, H
Southey, MC
Park, DJ

November 2013

The fulltext of this publication will be made publicly available after relevant embargo periods have...

Accurate Mutation Detection in Cancer Through Improved Error Suppression and Quantification of Molecular Complexity

Wang, Ting Ting

June 2018

DNA from cancer cells is often masked by nucleic acids from normal cells in tumour tissues and blood...

Overview of the Duplex Sequencing methodology.

Scott R. Kennedy (463286)
Jesse J. Salk (319884)
Michael W. Schmitt (463287)
Lawrence A. Loeb (335078)

September 2013

<p>(A) Adapter design with random double-stranded tag sequence and invariant spacer sequence. (B) Li...

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

James L. O’Donnell (3181911)
Ryan P. Kelly (255075)
Natalie C. Lowell (3181914)
Jesse A. Port (124035)

March 2016

<div><p>Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversi...

Additional file 1: Figure S1. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Abstract

Extracted data

Additional file 1: Figure S1. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

Abstract

Extracted data

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