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1. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Sinan Arslan, Francisco J. Garcia, Minghao Guo, Matthew W. Kellinger, Semyon Kruglyak, Jake A. LeVieux, Adeline H. Mah, Haosen Wang, Junhua Zhao, Chunhong Zhou, Andrew Altomare, John Bailey, Matthew B. Byrne, Chiting Chang, Steve X. Chen, Byungrae Cho, Claudia N. Dennler, Vivian T. Dien, Derek Fuller, Ryan Kelley, Omid Khandan, Michael G. Klein, Michael Kim, Bryan R. Lajoie, Bill Lin, Yu Liu, Tyler Lopez, Peter T. Mains, Andrew D. Price, Samantha R. Robertson, Hermes Taylor-Weiner, Ramreddy Tippana, Austin B. Tomaney, Su Zhang, Minna Abtahi, Mark R. Ambroso, Rosita Bajari, Ava M. Bellizzi, Chris B. Benitez, Daniel R. Berard, Lorenzo Berti, Kelly N. Blease, Angela P. Blum, Andrew M. Boddicker, Leo Bondar, Chris Brown, Chris A. Bui, Juan Calleja-Aguirre, Kevin Cappa, Joshua Chan, Victor W. Chang, Katherine Charov, Xiyi Chen, Rodger M. Constandse, Weston Damron, Mariam Dawood, Nicole DeBuono, John D. Dimalanta, Laure Edoli, Keerthana Elango, Nikka Faustino, Chao Feng, Matthew Ferrari, Keith Frankie, Adam Fries, Anne Galloway, Vlad Gavrila, Gregory J. Gemmen, James Ghadiali, Arash Ghorbani, Logan A. Goddard, Adriana Roginski Guetter, Garren L. Hendricks, Jendrik Hentschel, Daniel J. Honigfort, Yun-Ting Hsieh, Yu-Hsien Hwang Fu, Scott K. Im, Chaoyi Jin, Shradha Kabu, Daniel E. Kincade, Shawn Levy, Yu Li, Vincent K. Liang, William H. Light, Jonathan B. Lipsher, Tsung-li Liu, Grace Long, Rui Ma, John M. Mailloux, Kyle A. Mandla, Anyssa R. Martinez, Max Mass, Daniel T. McKean, Michael Meron, Edmund A. Miller, Celyne S. Moh, Rachel K. Moore, Juan Moreno, Jordan M. Neysmith, Cassandra S. Niman, Jesus M. Nunez, Micah T. Ojeda, Sara Espinosa Ortiz, Jenna Owens, Geoffrey Piland, Daniel J. Proctor, Josua B. Purba, Michael Ray, Daisong Rong, Virginia M. Saade, Sanchari Saha, Gustav Santo Tomas, Nicholas Scheidler, Luqmanal H. Sirajudeen, Samantha Snow, Gudrun Stengel, Ryan Stinson, Michael J. Stone, Keoni J. Sundseth, Eileen Thai, Connor J. Thompson, Marco Tjioe, Christy L. Trejo, Greg Trieger, Diane Ni Truong, Ben Tse, Benjamin Voiles, Henry Vuong, Jennifer C. Wong, Chiung-Ting Wu, Hua Yu, Yingxian Yu, Ming Yu, Xi Zhang, Da Zhao, Genhua Zheng, Molly He, and Michael Previte

Subjects
Biomedical Engineering, Molecular Medicine, Bioengineering, Applied Microbiology and Biotechnology, Biotechnology
Abstract

We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase–polymer–nucleotide complexes bound to clonal copies of DNA targets. These polymer–nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar and yield negligible dissociation rates. Avidity sequencing achieves high accuracy, with 96.2% and 85.4% of base calls having an average of one error per 1,000 and 10,000 base pairs, respectively. We show that the average error rate of avidity sequencing remained stable following a long homopolymer.

Published
2023
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2. Sequencing by Avidity Enables High Accuracy With Low Reagent Consumption

Author

Sinan Arslan, Matthew Kellinger, Semyon Kruglyak, Jake LeVieux, Adeline Mah, Haosen Wang, Junhua Zhao, Chunhong Zhou, John Bailey, Matthew Byrne, Chiting Chang, Steve Chen, Claudia Dennler, Samantha Dennler, Vivian Dien, Derek Fuller, Francisco Garcia, Minghao Guo, Ryan Kelley, Omid Khandan, Michael Klein, Michael Kim, Bill Lin, Yu Liu, Tyler Lopez, Peter Mains, Andrew Price, Hermes Taylor, Ramreddy Tippana, Austin Tomaney, Richard Zhang, Minna Abtahi, Mark Ambroso, Rosi Bajari, Ava Bellizi, Chris Benitez, Daniel Berard, Lorenzo Berti, Kelly Blease, Angela Blum, Andrew Boddicker, Leo Bondar, Chris Bui, Kevin Cappa, Joshua Chan, Victor Chang, Katia Charov, Xiyi Chen, Rodger Constandse, Weston Damron, Mariam Dawood, Nicole Debruno, John Dmalanta, Laure Edoli, Keerthi Elango, Nikka Faustino, Chao Feng, Matthew Ferrari, Kieth Frankie, Adam Fries, Anne Galloway, Vlad Gavrila, Gregory Gemmen, James Ghadiali, Logan Goddard, Adriana Roginski, Garren Hendricks, Jendrick Hentschel, Doris Hseih, Yu-Hsein Hwang-fu, Scott Im, Chaoyi Jin, Daniel Kincade, Bryan Lajooie, Shawn Levy, Yu Li, Vincent Liang, William Light, Jonathan Lipsher, Tsungli Liu, Guixia Long, Rui Ma, Jack Mailloux, Kyle Mandla, Anyssa Martinez, Max Mass, Michael Meron, Celyne Moh, Rachel Moore, Juan Moreno, Jordan Neysmith, Cassandra Niman, Jesus Nunez, Micah Ojeda, Jenna Owens, Sara Espinosa Ortiz, Geoffrey Piland, Dan Proctor, Josua Purba, Michael Ray, Daisong Rong, Virginia Saade, Sanchari Saha, Luqmanal Sirajudeen, Gudrun Stengel, Ryan Stinson, Michael Stone, Keoni Sundseth, Eileen Thai, Connor Thompson, Gustav Santo Tomas, Christy Trejo, Greg Trieger, Diane Truong, Ben Tse, Benjamin Voiles, Henry Vuong, Jennifer Wong, Chiung-Ting Wu, Hua Yu, Ming Yu, Cindy Zhang, Da Zhao, Frank Zheng, Molly He, and Michael Previte

Abstract

We present a novel sequencing chemistry implemented as part of the AVITI system. Relying on the proximal DNA binding sites created through DNA amplification on a solid support, avidity sequencing uses multivalent nucleotide ligands on dye-labeled cores to simultaneously form polymerase-polymer nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides by 100x and yield a negligible dissociation rate. We demonstrate the use of avidites within a novel sequencing technology that surpasses Q40 accuracy and enables a diversity of applications that include single cell RNA-seq and whole human genome sequencing.

Published
2022
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3. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Sinan Arslan, Francisco J. Garcia, Minghao Guo, Matthew W. Kellinger, Semyon Kruglyak, Jake A. LeVieux, Adeline H. Mah, Haosen Wang, Junhua Zhao, Chunhong Zhou, Andrew Altomare, John Bailey, Matthew B. Byrne, Chiting Chang, Steve X. Chen, Claudia N. Dennler, Vivian T. Dien, Derek Fuller, Ryan Kelley, Omid Khandan, Michael G. Klein, Michael Kim, Bryan R. Lajoie, Bill Lin, Yu Liu, Tyler Lopez, Peter T. Mains, Andrew D. Price, Samantha R. Robertson, Hermes Taylor-Weiner, Ramreddy Tippana, Austin B. Tomaney, Su Zhang, Mark R. Ambroso, Rosita Bajari, Ava M. Bellizzi, Chris B. Benitez, Daniel R. Berard, Lorenzo Berti, Kelly N. Blease, Angela P. Blum, Andrew M. Boddicker, Leo Bondar, Chris Brown, Chris A. Bui, Juan Calleja-Aguirre, Kevin Cappa, Joshua Chan, Victor W. Chang, Katherine Charov, Xiyi Chen, Rodger M. Constandse, Ryan Costello, Weston Damron, Mariam Dawood, Nicole DeBuono, John D. Dimalanta, Laure Edoli, Keerthana Elango, Nikka Faustino, Chao Feng, Mathhew Ferrari, Keith Frankie, Adam Fries, Anne Galloway, Vlad Gavrila, Gregory J. Gemmen, James Ghadiali, Arash Ghorbani, Logan A. Goddard, Adriana R. Guetter, Garren L. Hendricks, Jendrik Hentschel, Daniel J. Honigfort, Yun-Ting Hsieh, Yu-Hsien Hwang Fu, Scott K. Im, Chaoyi Jin, Shradha Kabu, Daniel E. Kincade, Shawn Levy, Yu Li, Vincent K. Liang, William H. Light, Jonathan B. Lipsher, Tsung-li Liu, Grace Long, Rui Ma, John M. Mailloux, Kyle A. Mandla, Anyssa R. Martinez, Max Mass, Daniel T. McKean, Michael Meron, Celyne S. Moh, Rachel K. Moore, Juan Moreno, Jordan M. Neysmith, Cassandra S. Niman, Jesus M. Nunez, Micah T. Ojeda, Sara Espinosa Ortiz, Jenna Owens, Geoffrey Piland, Daniel J. Proctor, Josua B. Purba, Michael Ray, Daisong Rong, Virginia M. Saade, Sanchari Saha, Gustav Santo Tomas, Nicholas Scheidler, Luqmanal H. Sirajudeen, Samantha Snow, Gudrun Stengel, Ryan Stinson, Michael J. Stone, Keoni J. Sundseth, Eileen Thai, Connor J. Thompson, Marco Tjioe, Christy L. Trejo, Greg Trieger, Diane Ni Truong, Ben Tse, Benjamin Voiles, Henry Vuong, Jennifer C. Wong, Chiung-Ting Wu, Hua Yu, Yingxian Yu, Ming Yu, Xi Zhang, Da Zhao, Genhua Zheng, Molly He, and Michael Previte

Abstract

We present avidity sequencing - a novel sequencing chemistry that separately optimizes the process of stepping along a DNA template and the process of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase-polymer nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar, and yield negligible dissociation rates. We demonstrate the use of avidites as a key component of a sequencing technology that surpasses Q40 accuracy and enables a diversity of applications that include single cell RNA-seq and whole human genome sequencing. We also show the advantages of this technology in sequencing through long homopolymers.

Published
2022
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4. How Serious is the Impact of Type II Diabetes in Rural Kenya?

Author

Ahmed Kasay, Hafsa Parpia, Changambi Mwamlole, Hemed El-busaidy, Mariam Dawood, and Nahida Koraya

Subjects
medicine.medical_specialty, Proteinuria, medicine.diagnostic_test, End organ damage, business.industry, Endocrinology, Diabetes and Metabolism, Physical examination, medicine.disease, Surgery, Diabetic nephropathy, Endocrinology, Internal medicine, Diabetes mellitus, medicine, medicine.symptom, Family history, business, Abdominal obesity, Sedentary lifestyle
Abstract

Over 50% of all adult hospital admissions and 55% of hospital deaths in Kenya are non-communicable, of which diabetes is among the leading. We aimed to describe the impact of type II diabetes at a rural community in Kenya. 200 healthy adult patients underwent random blood sucrose (RBS) testing after ethical approval by the Isiolo County Hospital. Diabetes was defined as RBS ≥11.1 mmol/l. A thorough history, physical examination and dipstick urinalysis for urine protein was done to identify risk factors and/or evidence of end organ damage. 32 patients (16%) had RBS ≥11.1 mmol/l. 12 patients (37.5%) never knew they were diabetic and those who knew 63% were not taking any medication. The most common risk factors were high fat diet (59.4%), sedentary lifestyle (46.8%) and family history of diabetes in first degree relative (37.5%). 43.7% of patients (n=14) had abdominal obesity while 21.9% (n=7) had various foot abnormalities. 8 patients (25%) had proteinuria of ≥ +1 on dipstick urinalysis. The 16% diabetes prevalence is among the highest recorded for a community living on ≤ 1 dollar/day. Further, evidence of end organ damage as depicted by massive proteinuria warrants urgent attention to this underprivileged group. It is hoped the results will form basis for future screening of diabetic nephropathy and other diabetes-related end organs involvement in this part of the world.

Published
2014
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