Granted Patent
B2
US 12,644,153 · App. 19/281,431 · Granted Jun 2, 2026
Methods and systems for monitoring a recipient of an allograft
Inventors:
Robert Woodward (Pleasanton, CA); Marica Grskovic (Burlingame, CA); James Yee (San Mateo, CA); Mitch Nelles (Half Moon Bay, CA); David Hiller (Brisbane, CA)
Assignee:
CareDx, Inc.
C12Q1/6876C12Q1/6806C12Q1/686C12Q1/6883G16B20/00C12Q2600/118C12Q2600/156C12Q2600/158G16H50/30Y02A90/10
View Patent ↗
Loading inventors, assignments & file history…
Abstract
Disclosed herein are methods for sequencing, comprising, providing a sample, wherein said sample comprises a plurality of nucleic acid (NA) molecules, isolating said plurality of NA molecules from said sample, amplifying said plurality of NA molecules, subjecting said plurality of NA molecules to one or more amplification reactions to generate a plurality of cDNA molecules, and sequencing said plurality of cDNA molecules or derivatives thereof. Also disclosed herein are systems, comprising, a processor, and a non-transitory computer readable storage medium encoded with a computer program that causes said processor to providing a sample, wherein said sample comprises a plurality of NA molecules, isolating said plurality of NA molecules from said sample, amplifying said plurality of NA molecules, subjecting said plurality of nucleic acid molecules to one or more amplification reactions to generate a plurality of cDNA molecules, and sequencing said plurality of cDNA molecules or derivatives thereof.
Claims (32)
1 . A method for detecting a plurality of amplified DNA molecules, comprising:
(a) providing a sample of a subject, wherein said sample comprises a plurality of cell-free nucleic acid molecules, and wherein said subject is a recipient of an allograft from a donor;
(b) isolating said plurality of cell-free nucleic acid molecules from said sample;
(c) amplifying said plurality of cell-free nucleic acid molecules using a plurality of primers to generate said plurality of amplified DNA molecules, wherein said plurality of primers target independent polymorphisms; and
(d) detecting said plurality of amplified DNA molecules, or derivatives thereof, wherein genotyping of said subject is not performed.
2 . The method of claim 1 , wherein said independent polymorphisms comprise single nucleotide polymorphisms (SNPs), insertions, or deletions.
3 . The method of claim 2 , wherein said independent polymorphisms comprise at least 10, at least 50, at least 100, or at least 200 independent SNPs, insertions, or deletions.
4 . The method of claim 2 , wherein said independent polymorphisms comprise single nucleotide polymorphisms (SNPs).
5 . The method of claim 4 , wherein said independent polymorphisms comprise at least 10, at least 50, at least 100, or at least 200 independent SNPs.
6 . The method of claim 4 , wherein each SNP has a minor allele frequency of at least 0.4.
7 . The method of claim 6 , wherein each SNP has an overall population minor allele frequency of at least 0.4.
8 . The method of claim 6 , wherein each SNP has a target population minor allele frequency of at least 0.4.
9 . The method of claim 4 , wherein each SNP has a genomic distance of greater than 500 kilobases.
10 . The method of claim 1 , wherein said plurality of cell-free nucleic acid molecules comprises cell-free DNA molecules.
11 . The method of claim 10 , wherein said plurality of cell-free DNA molecules comprises recipient-derived cell-free DNA molecules and donor-derived cell-free DNA molecules.
12 . The method of claim 1 , wherein said allograft is a solid organ, a tissue, or a cell transplant.
13 . The method of claim 1 , wherein said allograft is a kidney transplant, a liver transplant, a lung transplant, a heart transplant, a pancreas transplant, a cornea transplant, a skin tissue transplant, a skin cell transplant, an organ system transplant, a xenotransplant, or a combination thereof.
14 . The method of claim 1 , wherein said allograft is a heart transplant.
15 . The method of claim 1 , wherein said allograft is a kidney transplant.
16 . The method of claim 1 , wherein said allograft is a lung transplant.
17 . The method of claim 1 , wherein said sample is blood, serum, plasma, or urine.
18 . The method of claim 1 , wherein said sample is derived from blood.
19 . The method of claim 1 , wherein said sample is plasma.
20 . The method of claim 1 , wherein said amplifying comprises polymerase chain reaction (PCR).
21 . The method of claim 1 , further comprising purifying said plurality of amplified DNA molecules, or derivatives thereof.
22 . The method of claim 1 , further comprising barcoding said plurality of nucleic acid molecules.
23 . The method of claim 1 , wherein said detecting comprises detecting an optical signal from a probe coupled to an amplified DNA molecule, or a derivative thereof of said plurality of amplified DNA molecules, or derivatives thereof.
24 . The method of claim 1 , wherein said detecting comprises sequencing by high-throughput sequencing.
25 . The method of claim 24 , wherein said sequencing by high-throughput sequencing comprises next generation sequencing.
26 . The method of claim 1 , wherein genotyping of said donor is not performed.
27 . The method of claim 1 , further comprising outputting a status of said allograft based on said detecting of said plurality of amplified nucleic acid molecules.
28 . The method of claim 27 , wherein said status is a rejection of said allograft, or risk thereof.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Mar 3, 2026
From: WOODWARD, ROBERT; GRSKOVIC, MARICA; YEE, JAMES; NELLES, MITCH; HILLER, DAVID
To: CAREDX, INC.
Reel/Frame 073960/0468 →
Continuity (5)
Continuation
18936839
· Nov 4, 2024
Provisional Application
61953582
· Mar 14, 2014
References Cited (400)
US 5210015A
· Gelfand et al.
· 1993
[cited by applicant]
US 6132997A
· Shannon
· 2000
[cited by applicant]
US RE39920E
· Umansky et al.
· 2007
[cited by applicant]
US 7332277B2
· Dhallan
· 2008
[cited by applicant]
US 7604936B2
· Wohlgemuth et al.
· 2009
[cited by applicant]
US 7645575B2
· Wohlgemuth et al.
· 2010
[cited by applicant]
US 7655399B2
· Cantor et al.
· 2010
[cited by applicant]
US 7691569B2
· Wohlgemuth et al.
· 2010
[cited by applicant]
US 7727720B2
· Dhallan
· 2010
[cited by applicant]
US 7993832B2
· Rosenberg et al.
· 2011
[cited by applicant]
US 8024128B2
· Rabinowitz et al.
· 2011
[cited by applicant]
US 8515679B2
· Rabinowitz et al.
· 2013
[cited by applicant]
US 8532930B2
· Rabinowitz et al.
· 2013
[cited by applicant]
US 8706422B2
· Lo et al.
· 2014
[cited by applicant]
US 8825412B2
· Rabinowitz et al.
· 2014
[cited by applicant]
US 9370689B2
· Guillama et al.
· 2016
[cited by applicant]
US 9499870B2
· Babiarz et al.
· 2016
[cited by applicant]
US 9639657B2
· Rabinowitz et al.
· 2017
[cited by applicant]
US 9677118B2
· Zimmermann et al.
· 2017
[cited by applicant]
US 20020197621A1
· Drmanac
· 2002
[cited by applicant]
US 20020197630A1
· Knapp et al.
· 2002
[cited by applicant]
US 20040137470A1
· Dhallan
· 2004
[cited by applicant]
US 20060228721A1
· Leamon et al.
· 2006
[cited by applicant]
US 20070027636A1
· Rabinowitz
· 2007
[cited by applicant]
US 20070095905A1
· Kadaba
· 2007
[cited by applicant]
US 20070178501A1
· Rabinowitz et al.
· 2007
[cited by applicant]
US 20070248978A1
· Lal et al.
· 2007
[cited by applicant]
US 20100120038A1
· Mir et al.
· 2010
[cited by applicant]
US 20100151471A1
· Faham et al.
· 2010
[cited by applicant]
US 20100285478A1
· Chen et al.
· 2010
[cited by applicant]
US 20110033862A1
· Rabinowitz et al.
· 2011
[cited by applicant]
US 20110092763A1
· Rabinowitz et al.
· 2011
[cited by applicant]
US 20110173023A1
· LeClair et al.
· 2011
[cited by applicant]
US 20120185176A1
· Rabinowitz et al.
· 2012
[cited by applicant]
US 20120295810A1
· Quake et al.
· 2012
[cited by applicant]
US 20130024127A1
· Stuelpnagel et al.
· 2013
[cited by applicant]
US 20130123120A1
· Zimmermann et al.
· 2013
[cited by applicant]
US 20130173028A1
· Felty et al.
· 2013
[cited by applicant]
US 20130196862A1
· Rabinowitz et al.
· 2013
[cited by applicant]
US 20140051585A1
· Prosen et al.
· 2014
[cited by applicant]
US 20140065621A1
· Mhatre et al.
· 2014
[cited by applicant]
US 20140088995A1
· Damani
· 2014
[cited by applicant]
US 20140206552A1
· Rabinowitz et al.
· 2014
[cited by applicant]
US 20150154352A1
· Johnson et al.
· 2015
[cited by applicant]
US 20150203916A1
· Ikonomidis et al.
· 2015
[cited by applicant]
US 20160115541A1
· Schutz et al.
· 2016
[cited by applicant]
US 20160371428A1
· Ryan et al.
· 2016
[cited by applicant]
US 20160371432A1
· Rabinowitz et al.
· 2016
[cited by applicant]
US 20180173845A1
· Sigurjonsson et al.
· 2018
[cited by applicant]
US 20180173846A1
· Sigurjonsson et al.
· 2018
[cited by applicant]
US 20180344215A1
· Ohnemus et al.
· 2018
[cited by applicant]
US 20190125799A1
· Konto et al.
· 2019
[cited by applicant]
US 20190153521A1
· Mitchell et al.
· 2019
[cited by applicant]
US 20190185913A1
· Zimmermann et al.
· 2019
[cited by applicant]
US 20190203264A1
· Quake et al.
· 2019
[cited by applicant]
US 20190367972A1
· Mitchell et al.
· 2019
[cited by applicant]
US 20200032340A1
· Mitchell et al.
· 2020
[cited by applicant]
US 20200109449A1
· Stamm et al.
· 2020
[cited by applicant]
US 20200165678A1
· Mitchell et al.
· 2020
[cited by applicant]
US 20210037813A1
· Scalea et al.
· 2021
[cited by applicant]
US 20210139983A1
· Mitchell et al.
· 2021
[cited by applicant]
US 20210139988A1
· Mitchell et al.
· 2021
[cited by applicant]
US 20210257048A1
· Zimmermann et al.
· 2021
[cited by applicant]
US 20210327538A1
· Egilsson et al.
· 2021
[cited by applicant]
US 20210395835A1
· Grskovic et al.
· 2021
[cited by applicant]
US 20220025459A1
· Schütz et al.
· 2022
[cited by applicant]
US 20220042100A1
· Zhang et al.
· 2022
[cited by applicant]
US 20220051803A1
· Nelson
· 2022
[cited by applicant]
US 20220056534A1
· Rivers et al.
· 2022
[cited by applicant]
US 20220073989A1
· Sarwal et al.
· 2022
[cited by applicant]
US 20220081715A1
· Naesens et al.
· 2022
[cited by applicant]
US 20220093208A1
· Lefkowitz et al.
· 2022
[cited by applicant]
US 20220098650A1
· Slater
· 2022
[cited by applicant]
US 20220145391A1
· Mitchell et al.
· 2022
[cited by applicant]
US 20220154249A1
· Zimmermann et al.
· 2022
[cited by applicant]
US 20220267849A1
· Mitchell et al.
· 2022
[cited by applicant]
US 20220340963A1
· North et al.
· 2022
[cited by applicant]
US 20220356521A1
· Woodward et al.
· 2022
[cited by applicant]
US 20220356522A1
· Mitchell et al.
· 2022
[cited by applicant]
US 20220356526A1
· Babiarz et al.
· 2022
[cited by applicant]
US 20220356530A1
· Sharma et al.
· 2022
[cited by applicant]
US 20220392568A1
· Newbound et al.
· 2022
[cited by applicant]
US 20230167499A1
· Mitchell et al.
· 2023
[cited by applicant]
US 20230203573A1
· Swenerton et al.
· 2023
[cited by applicant]
US 20230257816A1
· Mitchell et al.
· 2023
[cited by applicant]
US 20230257822A1
· De Vlaminck et al.
· 2023
[cited by applicant]
US 20230287497A1
· Moshkevich et al.
· 2023
[cited by applicant]
US 20230343411A1
· Rabinowitz et al.
· 2023
[cited by applicant]
US 20230348985A1
· Clark-Langone et al.
· 2023
[cited by applicant]
US 20230352144A1
· Zhang et al.
· 2023
[cited by applicant]
US 20230360723A1
· Rabinowitz et al.
· 2023
[cited by applicant]
US 20230368865A1
· Rabinowitz et al.
· 2023
[cited by applicant]
US 20230395258A1
· Qu et al.
· 2023
[cited by applicant]
US 20230399694A1
· Woodward et al.
· 2023
[cited by applicant]
US 20230399695A1
· Woodward et al.
· 2023
[cited by applicant]
US 20230399696A1
· Woodward et al.
· 2023
[cited by applicant]
US 20230407392A1
· Woodward et al.
· 2023
[cited by applicant]
US 20230407393A1
· Woodward et al.
· 2023
[cited by applicant]
US 20230407394A1
· Woodward et al.
· 2023
[cited by applicant]
US 20230407395A1
· Woodward et al.
· 2023
[cited by applicant]
US 20230407396A1
· Woodward et al.
· 2023
[cited by applicant]
US 20240038328A1
· Rabinowitz et al.
· 2024
[cited by applicant]
US 20240132960A1
· Demko et al.
· 2024
[cited by applicant]
US 20250388965A1
· Woodward et al.
· 2025
[cited by applicant]
CA 2668608A1
· 2008
[cited by applicant]
CN 102618626A
· 2012
[cited by applicant]
CN 103374518A
· 2013
[cited by applicant]
CN 106536752A
· 2017
[cited by applicant]
EP 3712898A1
· 2020
[cited by applicant]
WO WO2010009398A1
· 2010
[cited by applicant]
WO WO2011057061A1
· 2011
[cited by applicant]
WO WO2012019193A2
· 2012
[cited by applicant]
WO WO2012019200A2
· 2012
[cited by applicant]
WO WO2013043922A1
· 2013
[cited by applicant]
WO WO2013049892A1
· 2013
[cited by applicant]
WO WO2013159035A2
· 2013
[cited by applicant]
WO WO2014074501A1
· 2014
[cited by applicant]
WO WO2014116729A2
· 2014
[cited by applicant]
WO WO2014180910A1
· 2014
[cited by applicant]
WO WO2014194113A2
· 2014
[cited by applicant]
WO WO2015069933A1
· 2015
[cited by applicant]
WO WO2015085350A1
· 2015
[cited by applicant]
WO WO2015138997A1
· 2015
[cited by applicant]
WO WO2016176662A1
· 2016
[cited by applicant]
WO WO2016201507A1
· 2016
[cited by applicant]
WO WO2017129756A1
· 2017
[cited by applicant]
WO WO2018000031A1
· 2018
[cited by applicant]
WO WO2018187226A1
· 2018
[cited by applicant]
WO WO2018236827A1
· 2018
[cited by applicant]
WO WO2018236911A1
· 2018
[cited by applicant]
WO WO2020172164A1
· 2020
[cited by applicant]
WO WO2021021657A1
· 2021
[cited by applicant]
WO WO2021084486A1
· 2021
[cited by applicant]
WO WO2021257883A1
· 2021
[cited by applicant]
WO WO2022232439A1
· 2022
[cited by applicant]
WO WO2023043956A1
· 2023
[cited by applicant]
WO WO2023116717A1
· 2023
[cited by applicant]
Access Array™ Barcode Library for Illumina Sequencers—384 (Bidirectional); Standard BioTools™. PN100-3771. 3 pages (2023).
[cited by applicant]
Access Array System for Illumina Sequencing Systems: User guide. PN 100-3770 M1. Fluidigm Corporation. 90 pages (2019).
[cited by applicant]
Aftab, Blake T. et al., Toward “off-the-shelf” allogeneic CAR T cells. Advances in Cell and Gene Therapy, 3(3):e86, 11 pages (2020).
[cited by applicant]
Agbor-Enoh Sean et al., Circulating cell-free DNA as a biomarker of tissue injury: Assessment in a cardiac xenotransplantation model. Journal of Heart and Lung Transplantation. 37(8):967-975 (2018).
[cited by applicant]
Akalin, Enver et al., Clinical Validation of an Immune Quiescence Gene Expression Signature in Kidney Transplantation. Kidney360. 2(12):1998-2009 (2021).
[cited by applicant]
Akbari, Parsa Biological and Aetiological Inference from the Statistical Genetic Analyses of Blood Cell Traits. Dissertation, Univ. of Cambridge, 210 pages (2020). available online at https://www.repository.cam.ac.uk/ha…
[cited by applicant]
Al Turki, Saeed. Integrated approaches to elucidate the genetic architecture of congenital heart defects. Dissertation, University of Cambridge. 302 pages (2014). available online at https://www.repository.cam.ac.uk/han…
[cited by applicant]
Alasoo, Kaur et al. Genetic effects on promoter usage are highly context-specific and contribute to complex traits. eLife, 8:e41673, 23 pages (2019).
[cited by applicant]
Anazawa, Takayuki et al., Current state and future evolution of pancreatic islet transplantation. Annals of Gastroenterological Surgery. 3(1):34-42 (2019).
[cited by applicant]
Ariosa Diagnostics, Inc.: short description of company and founders. Available online at https://relationshipscience.com/organization/ariosa-diagnostics-inc-1733841, accessed on Nov. 22, 2021, 1 page.
[cited by applicant]
Bader, P. et al. How and when should we monitor chimerism after allogeneic stem cell transplantation?. Bone marrow transplantation 35(2):107-119 (2005).
[cited by applicant]
Barker et al., “Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel,” Genome Res., 14(5):901-917, (2004).
[cited by applicant]
Barker, Juliet N. et al. Transplantation of 2 partially HLA-matched umbilical cord blood units to enhance engraftment in adults with hematologic malignancy. Blood 105(3):1343-1347 (2005).
[cited by applicant]
Bay, Jakob T. et al., Low C4 gene copy numbers are associated with superior graft survival in patients transplanted with a deceased donor kidney et al., , Kidney International. 84(3):562-569 (2013).
[cited by applicant]
Beck, Julia et al. Digital droplet PCR for rapid quantification of donor DNA in the circulation of transplant recipients as a potential universal biomarker of graft injury. Clinical Chemistry 59(12):1732-1741 (2013).
[cited by applicant]
Belkadi, Aziz et al., Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions. PLoS ONE 16(4):e0249930, 17 pages (2021).
[cited by applicant]
Beszteri, Bánk et al., Average genome size: a potential source of bias in comparative metagenomics. The ISME Journal 4(8):1075-1077 (2010).
[cited by applicant]
Biswas, Chandra S. et al., Double Haploidentical Hematopoietic Stem Cell Transplantation Results in Successful Engraftment of Bone Marrow from Both Donors without Graft-versus-Host or Graft-versus-Graft Effects. Biol Bl…
[cited by applicant]
Bloom, Roy D. et al. Cell-free DNA and active rejection in kidney allografts. Journal of the American Society of Nephrology 28(7):2221-2232 (2017).
[cited by applicant]
Bossini-Castillo, Lara et al., Immune disease variants modulate gene expression in regulatory CD4+ T cells and inform drug targets. bioRxiv, 654632. 29 pages (2019).
[cited by applicant]
Brodin, Johanna et al., PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data. PLOS One, 8(7):e70388, 7 pages (2013).
[cited by applicant]
Broman, Karl W et al., Identification and Correction of Sample Mix-Ups in Expression Genetic Data: A Case Study. G3: Genes, Genomes, Genetics. 5(10):2177-2186 (2015).
[cited by applicant]
Cameron-Christie, Sophia et al., Exome-Based Rare-Variant Analyses in CKD. Journal of the American Society of Nephrology 30(6):1109-1122, 35 pages 9 (2019).
[cited by applicant]
CareDx, (Dec. 2-10, 2020). “Abstract Submission: Universal Sensitive, Accurate and Precise Microchimerism Surveillance Solution for Allogeneic Hematopoietic Cell Transplant,” 62nd ASH Annual Meeting, 7 pages.
[cited by applicant]
CareDx, (Dec. 2-10, 2020). “Poster Presentation: Universal Sensitive, Accurate and Precise Microchimerism Surveillance Solution for Allogeneic Hematopoietic Cell Transplant,” 62nd ASH Annual Meeting, 12 pages.
[cited by applicant]
CareDx, (Feb. 8-12, 2021). “Abstract Session: A Sensitive and Precise Universal Surveillance Solution for Pharmacokinetic Monitoring of Off-the-Shelf Cell Therapies,” TCT, Transplantation & Cellular Therapy Meetings of …
[cited by applicant]
CareDx, (Feb. 8-12, 2021). “Abstract Session: Post-Allogeneic HCT Microchimerism Monitoring Solution with High Accuracy and Sensitivity,” TCT, Transplantation & Cellular Therapy Meetings of ASTCT and CIBMTR, 17 pages.
[cited by applicant]
CareDx, (Feb. 8-12, 2021). “Poster Presentation: A Sensitive and Precise Universal Surveillance Solution for Pharmacokinetic Monitoring of Off-the-Shelf Cell Therapies,” TCT, Transplantation & Cellular Therapy Meetings …
[cited by applicant]
CareDx, (Feb. 8-12, 2021). “Poster Presentation: Post-Allogeneic HCT Microchimerism Monitoring Solution with High Accuracy and Sensitivity,” TCT, Transplantation & Cellular Therapy Meetings of ASTCT and CIBMTR, 1 page.
[cited by applicant]
Cassuto, James R. et al., Kidney transplantation in patients with a prior heart transplant et al., Transplantation 89(4): 427-433 (2010).
[cited by applicant]
Cha, Rita S. and Thilly, William G. Specificity, efficiency, and fidelity of PCR. Genome Research 3(3): S18-S29. (1993).
[cited by applicant]
Chen, Lu et al., Transcriptional diversity during lineage commitment of human blood progenitors. Science. 345(6204):1251033, 25 pages (2014).
[cited by applicant]
Chen, Yan. et al. Peripheral blood transcriptome sequencing reveals rejection-relevant genes in long-term heart transplantation. International Journal of Cardiology 168(3):2726-2733 (2013).
[cited by applicant]
Cheng, Jing et al., Exome sequencing identifies a novel frameshift mutation of MY06 as the cause of autosomal dominant nonsyndromic hearing loss in a Chinese family, Ann Hum Genet., 78(6):410-423 (2014).
[cited by applicant]
Chiu, Rossa W. K., et al., Effects of blood-processing protocols on fetal and total DNA quantification in maternal plasma. Clinical Chemistry. 47(9):1607-1613 (2001).
[cited by applicant]
Christakoudi, Sofia. et al. Development of a multivariable gene-expression signature targeting T-cell-mediated rejection in peripheral blood of kidney transplant recipients validated in cross-sectional and longitudinal …
[cited by applicant]
Chu, Tianjiao et al., A novel approach toward the challenge of accurately quantifying fetal DNA in maternal plasma. Prenatal Diagnosis. 30(12-13):1226-1229 (2010).
[cited by applicant]
Cirulli, Elizabeth T. et al., Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways. Science, 347(6229):1436-1441, 18 pages (2015).
[cited by applicant]
Colobran, R. et al. Copy number variation in the CCL4L gene is associated with susceptibility to acute rejection in lung transplantation. Genes & Immunity 10(3):254-259 (2009).
[cited by applicant]
Cooper, David K. A brief history of cross-species organ transplantation. Proc Baylor Univ Med Ctr. 25(1):49-57 (2012).
[cited by applicant]
Co-pending U.S. Appl. No. 18/935,347, inventors Woodward; Robert et al., filed Nov. 1, 2024.
[cited by applicant]
Co-pending U.S. Appl. No. 18/935,348, inventors Woodward; Robert et al., filed Nov. 1, 2024.
[cited by applicant]
Co-pending U.S. Appl. No. 18/935,360, inventors Woodward; Robert et al., filed Nov. 1, 2024.
[cited by applicant]
Co-pending U.S. Appl. No. 18/936,839, inventors Woodward; Robert et al., filed Nov. 4, 2024.
[cited by applicant]
Co-pending U.S. Appl. No. 18/936,845, inventors Woodward; Robert et al., filed Nov. 4, 2024.
[cited by applicant]
Crespo-Leiro Utility of Gene Expression Profiling Test (GEP) Score Instability to Predict Future Clinical Outcomes in Heart Transplant: Results from the CARGO 2 European-Based Multicenter Trial. The Journal of Heart and…
[cited by applicant]
Crespo-Leiro, M. et al. Increased Plasma Levels of Donor-Derived Cell-Free DNA Correlate with Rejection in Heart Transplant Recipients: The CARGO II Multicenter Trial. The Journal of Heart and Lung Transplantation 34(4)…
[cited by applicant]
Davey, John W. et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12(7):499-510 (2011).
[cited by applicant]
DbSNP—Submitted SNP(ss) details: ss1341432998, submitted Aug. 16, 2014. 2 pages (2014). Available at: https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ss.cgi?subsnp_id=ss1341432998.
[cited by applicant]
DbSNP Short Genetic Variations_Reference SNP (rs) Report; rs1047979. 12 pages, released Sep. 21, 2022. Retrieved from https://www.ncbi.nlm.nih.gov/snp/rs1047979.
[cited by applicant]
De Vlaminck, Iwijn. et al. Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. Science translational medicine 6(241):241ra77, 1-8 (2014).
[cited by applicant]
Dedrick, Russell L. Understanding gene expression patterns in immune-mediated disorders. Journal of Immunotoxicology 4(3):201-207 (2007).
[cited by applicant]
Deng, M. C. et al. Noninvasive discrimination of rejection in cardiac allograft recipients using gene expression profiling. American Journal of Transplantation 6(1):150-160 (2006).
[cited by applicant]
Deng, Yangyang et al. Quantification of Circulating Pig-Specific DNA in the Blood of a Xenotransplantation Model. J. Vis. Exp 163:e61579, 1-12 (2020).
[cited by applicant]
Devonshire, Alison et al, Towards standardisation of cell-free DNA measurement in plasma: controls for extraction efficiency, fragment size bias and quantification. Anal Bioanal Chemistry. 406(26):6499-6512 (2014).
[cited by applicant]
Dhallan, Ravinder et al., A non-invasive test for prenatal diagnosis based on fetal DNA present in maternal blood: a preliminary study. Lancet. 369(9560):474-481 (2007).
[cited by applicant]
Dharnidharka, Vikas R, and Andrew Malone. Biomarkers to detect rejection after kidney transplantation. Pediatric Nephrology 33(7):1113-1122 (2018). Published online on Jun. 19, 2017.
[cited by applicant]
Do, Ron et al., Exome sequencing and complex disease: practical aspects of rare variant association studies. Human Molecular Genetics. 21(R1):R1-R9 (2012).
[cited by applicant]
Do, Ron et al., Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Research letter 9 pages (2014). doi:10/1038/nature13917.
[cited by applicant]
Do, Ron et al., Multiple rare alleles at LDLR and APOA5 confer risk for early-onset myocardial infection. Nature, 518(7537):102-106 (2015).
[cited by applicant]
Dobin, Alexander et al., STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 29(1):15-21 (2013).
[cited by applicant]
Egidio, Camila. et al. Universal Sensitive, Accurate and Precise Microchimerism Surveillance Solution for Allogeneic Hematopoietic Cell Transplant. Blood 136:32-33 (2020).
[cited by applicant]
EP3117012 D-19—Comparison of panels of SNPs disclosed D6, in the priority application (P) and in the application as filed (R). 51 pages, dated Mar. 10, 2021.
[cited by applicant]
EP3117012 Interloculory Decision in Opposition proceedings. 67 pages, dated Jun. 16, 2021.
[cited by applicant]
EP3117012 European Patent Office, Decision of Technical Board of Appeal 3.3.08, Case No. T 1514/21, dated Sep. 12, 2023.
[cited by applicant]
EP15761889.3 Extended European Search Report. 10 pages, dated Jul. 28, 2017.
[cited by applicant]
EP3117012 Communication of a notice of Opposition. 47 pages, dated Nov. 26, 2019.
[cited by applicant]
EP3117012 Notice of opposition to a European patent. 5 pages, dated Nov. 20, 2019.
[cited by applicant]
EP3117012 Statement of Facts and Arguments in support of Opposition. 24 pages, dated Nov. 20, 2019.
[cited by applicant]
EP3117012 Submission in Opposition Proceedings. 13 pages, dated Mar. 11, 2021.
[cited by applicant]
EP3117012 Letter from the Proprietor of patent. 50 pages, dated May 12, 2020.
[cited by applicant]
EP3117012 Minutes-of-the Oral Proceedings before the Opposition Division. 7 pages, dated Jul. 14, 2021.
[cited by applicant]
EP3117012 Proprietor Notice of Appeal Submission. 2 pages, dated Sep. 23, 2021.
[cited by applicant]
EP3117012 Proprietor Submission in Opposition Proceedings. 9 pages, dated Mar. 11, 2021.
[cited by applicant]
EP3117012 Proprietor Submission in Opposition Proceedings. 34 pages, dated Nov. 24, 2021.
[cited by applicant]
EP3117012 PubMed search for the terms “low linkage disequilibrium” and “SNPs” in publications before the filing date of the patent, submitted before the European Patent Office to Opposition. 6 pages, dated Mar. 11, 2021.
[cited by applicant]
EP3117012 Annex: Grounds of Opposition. 44 pages, dated Nov. 20, 2019.
[cited by applicant]
EP3117012 Communication of a notice of opposition. 178 pages, dated Nov. 25, 2019.
[cited by applicant]
EP3117012 Letter accompanying subsequently filed items. 3 pages, dated Sep. 14, 2021.
[cited by applicant]
EP3117012 Notice of opposition to a European patent. 6 pages, dated Nov. 20, 2019.
[cited by applicant]
EP3117012 Written Submissions pursuant to Rule 116 EPC in Opposition Proceedings. 46 pages, dated Mar. 10, 2021.
[cited by applicant]
EP3117012 Submission in Opposition Proceedings. 24 pages, dated Nov. 18, 2021.
[cited by applicant]
EP3117012 European Patent Office to Opposition. 16 pages, dated Jul. 30, 2020.
[cited by applicant]
EP3117012 Sworn statement by co-inventor Robert Woodward submitted before the European Patent Office to Opposition, 6 pages, dated May 5, 2020.
[cited by applicant]
EP3117012 Certificate of amendment of “XDX, Inc.” to “CAREDX, Inc.” submitted before the European Patent Office in Opposition, 2 pages. dated May 4, 2020.
[cited by applicant]
Federal Register vol. 76, No. 27 Feb. 9, 2011 7162-7175.
[cited by applicant]
Feng, Kai-chao. et al. Cocktail treatment with EGFR-specific and CD133-specific chimeric antigen receptor-modified T cells in a patient with advanced cholangiocarcinoma. Journal of hematology & oncology 10:4, 1-11 (2017…
[cited by applicant]
Fesnak, Andrew D. et al. Production of Chimeric Antigen Receptor T cells. Poster Presented at Nature Protocols. p. 1 (2017).
[cited by applicant]
Fievet, Alice et al., ART-DeCo: easy tool for detection and characterization of cross-contamination of DNA samples in diagnostic next-generation sequencing analysis. European Journal of Human Genetics. 27:792-800 (2019).
[cited by applicant]
Flickinger, Matthew et al., Correcting For Sample Contamination in Genotype Calling of DNA Sequence Data. AJHG, 97(2):284-290 (2015).
[cited by applicant]
Forshew, Tim. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Science Translational Medicine 4(136):136ra68, 1-12 (2012).
[cited by applicant]
Forshew, Tim. et al. Supplemental Information: Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Science Translational Medicine 4(136):136ra68, 1-20 (2012).
[cited by applicant]
Francalacci, Paolo et al., Low-Pass DNA Sequencing of 1200 Sardinians reconstructs European Y-Chromosome Phylogeny. Science. 341(6145):565-569 (2013).
[cited by applicant]
Frazer, Kelly A. et al., A second generation human haplotype map of over 3.1 million SNPs. Nature, 449(7164):851-861, (2007).
[cited by applicant]
Fu, Qiang. et al. An unbiased machine learning exploration reveals gene sets predictive of allograft tolerance after kidney transplantation. Frontiers in Immunology 12:695806, 1-10 (2021).
[cited by applicant]
Gadi, Vijayakrishna K. et al. Soluble donor DNA and islet injury after transplantation. Transplantation 92(5):607-611 (2011).
[cited by applicant]
Galli, Cesare. Animal Engineering for xenotransplantation. European Journal of Transplantation, Special Issue 1: 182-191 (2023).
[cited by applicant]
Garbern, Jessica et al., Cardiac Stem Cell Therapy and the Promise of Heart Regeneration, Cell Stem Cell, 12(6):689-698 (2013).
[cited by applicant]
Garcia, Marco Antonio Ayala et al., The major histocompatibility complex in transplantation. Journal of Transplantation. 20:842141, 7 pages (2012).
[cited by applicant]
Garcia Moreira, Vanessa. et al. Cell-free DNA as a noninvasive acute rejection marker in renal transplantation. Clinical Chemistry 55(11):1958-1966 (2009).
[cited by applicant]
Garg, Neetika. Donor-derived cell-free DNA: is it all the same? The jury is still out. Kidney 360. 1(10):1036-1037 (2020).
[cited by applicant]
Gargis Amy S.et al., Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nature Biotechnology. 33:689-693 (2015).
[cited by applicant]
Genome of the Netherlands Consortium: Francioli et al., (2014). “Whole-genome sequence variation, population structure and demographic history of the Dutch population,” Nat Genet., 46(8):818-825, 11 pages.
[cited by applicant]
Genotype: Definition. Nature, 2023; [retrieved on Jun. 23, 2025]. Available at URL: http;//www.nature.com/scitable/definition/genotype-234 pp. 1-2.
[cited by applicant]
Genotyping methods and solutions: Cutting-edge sequencing and microarray technologies for analyzing genetic variation. Illumina, 2015; [retrieved on Jun. 23, 2025]. Available at URL: http://www.illumina.com/techniques/p…
[cited by applicant]
Gielis E. M. et al., Cell-Free DNA: An Upcoming Biomarker in Transplantation. American Journal of Transplantation. 15(10):2541-2551, (May 2015).
[cited by applicant]
Gilly, Arthur et al., Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits. Nature Communications. 9:4674, 9 pages (2018).
[cited by applicant]
Gotoh, Mitsukazu. et al. Multiple donor allotransplantation: a new approach to pancreatic islet transplantation. Transplantation 45(6):1008-1011 (1988).
[cited by applicant]
Gotoh, Takahiro et al., Prediction of MYCN amplification in neuroblastoma using serum DNA and real-time quantitative polymerase chain reaction. J Clin Oncology. 23(22):5205-5210 (2005).
[cited by applicant]
Grinyo, Josep. et al. Association of four DNA polymorphisms with acute rejection after kidney transplantation. Transplant International 21(9):879-891 (2008).
[cited by applicant]
Grskovic, Marica et al., Validation of a Clinical-Grade Assay to Measure Donor-Derived Cell-Free DNA in Solid Organ Transplant Recipients, The Journal of Molecular Diagnostics, 18(6):890-902 (2016).
[cited by applicant]
Han, Dongmei. et al. Assessment of cytotoxic lymphocyte gene expression in the peripheral blood of human islet allograft recipients: elevation precedes clinical evidence of rejection. Diabetes 53(9):2281-2290 (2004).
[cited by applicant]
Hanvesakul, Rajesh. et al. Donor HLA-C genotype has a profound impact on the clinical outcome following liver transplantation. American Journal of Transplantation 8(9):1931-1941 (2008).
[cited by applicant]
Hara Hidetaka and Cooper, David K.C. Xenotransplantation—the future of corneal transplantation? Cornea 30(4):371-378 (2011).
[cited by applicant]
Hatzimichael, Eleftheria et al., Hematopoietic stem cell transplantation. Stem Cells and Cloning. 3:105-117 (2010).
[cited by applicant]
Hendricks, Audrey E. Use of appropriate controls in rare-variant studies. Book chapter in Assessing rare variation in complex traits, Springer, 14 pages (2015).
[cited by applicant]
Hendricks, Audrey E. et al., Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity. Scientific Report. 7:4394, 14 pages (2017).
[cited by applicant]
Hidestrand, Mats et al., Highly Sensitive Noninvasive Cardiac Transplant Rejection Monitoring Using Targeted Quantification of Donor-Specific Cell-Free Deoxyribonucleic Acid, Journal of the American College of Cardiolog…
[cited by applicant]
Hochberg, Ephraim P. et al. A novel rapid single nucleotide polymorphism (SNP)-based method for assessment of hematopoietic chimerism after allogeneic stem cell transplantation. Blood, The Journal of the American Societ…
[cited by applicant]
Hollander, Zsuzsanna et al., Whole blood biomarkers of acute cardiac allograft rejection: double-crossing the biopsy. Transplantation 90(12):1388-1393 (2010).
[cited by applicant]
Huang, Jinyan et al., A tool for RNA sequencing sample identity check. Bioinformatics. 29(11):1463-1464 (2013).
[cited by applicant]
Huang, Zheng et al., A novel method for detecting contaminated sample based on Illumina sequencing data, International Journal of Bioscience, Biochemistry and Bioinformatics. 4(2):116-120 (2014).
[cited by applicant]
Hummert, C et al. Creation and comparison of different chip definition files for Affymetrix microarrays. International Conference on Bioinformatics and Computational Biology. BIOCOMP'11. pp. 16-22 (2011).
[cited by applicant]
International HapMap Consortium, A second generation human haplotype map of over 3.1 million SNPs. Nature. 449(7164):851-861, 12 pages (2007).
[cited by applicant]
PCT/US2015/020603 International Preliminary Report on Patentability dated Sep. 22, 2016.
[cited by applicant]
PCT/US2015/020603 International Search Report and Written Opinion dated Jun. 29, 2015.
[cited by applicant]
Invivioscribe, Instructions for Use Amplification Control. General Purpose Reagent :1-13 (2020).
[cited by applicant]
Irion, Stefan et al., Bringing Neural Cell Therapies to the Clinic: Past and Future Strategies, Mol Ther Methods Clin Dev., 4:72-82 (2016).
[cited by applicant]
Jiang et al., FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. Bioinformatics, 28(22):2883-2890 (2012).
[cited by applicant]
Jiang, Peiyong, et al. FetalQuant
[cited by applicant]
Jorgez, Carolina J. et al., Quantity versus quality: Optimal methods for cell-free DNA isolation from plasma of pregnant women. Genetics in Medicine. 8(10):615-619 (2006).
[cited by applicant]
Judson, Robert N. et al., Towards stem cell therapies for skeletal muscle repair. NPJ Regen Med., 5:10, 6 pages (2020).
[cited by applicant]
Jun, Goo et al., An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res., 25:918-925 (2015).
[cited by applicant]
Jun, Goo. et al. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. The American Journal of Human Genetics 91(5):839-848 (2012).
[cited by applicant]
Jun, Goo. et al. Supplemental Information: Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. The American Journal of Human Genetics 91(5):839-848 (2012).
[cited by applicant]
Kamboj, Mini. et al. The changing epidemiology of vancomycin-resistant Enterococcus (VRE) bacteremia in allogeneic hematopoietic stem cell transplant (HSCT) recipients. Biology of Blood and Marrow Transplantation 16(11)…
[cited by applicant]
Kang et al., (2018). “Multiplexed droplet single-cell RNA-sequencing using natural genetic variation,” Nat Biotechnol., 38(11):1356, 19 pages.
[cited by applicant]
Kanwar, Manreet K. et al. Impact of cytomegalovirus infection on gene expression profile in heart transplant recipients. The Journal of Heart and Lung Transplantation 40(2):101-107 (2021). Published Online on Nov. 22, 2…
[cited by applicant]
Kim, Jieun. et al. SNP-based next-generation sequencing reveals low-level mixed chimerism after allogeneic hematopoietic stem cell transplantation. Annals of Hematology 97(9):1731-1734 (2018).
[cited by applicant]
Klein, Jan et al., The HLA system: first of two parts. Advances in Immunology, The New England Journal of Medicine. 343(10):702-709 (2000).
[cited by applicant]
Kunkel, Thomas A. and Bebenek, Katarzyna. DNA Replication Fidelity. Annual Reviews of Biochemistry. 69:497-529 (2000).
[cited by applicant]
Kurian, S. M. et al. Molecular classifiers for acute kidney transplant rejection in peripheral blood by whole genome gene expression profiling. American Journal of Transplantation 14(5):1164-1172 (2014).
[cited by applicant]
Langdon, (2014). “Mycoplasma contamination in the 1000 Genomes Project,” BioData Mining, 7:3, 13 pages.
[cited by applicant]
Laurence et al. (2014). “Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes,” PLoS ONE, 9(5):e97876, 8 pages.
[cited by applicant]
Lawson et al., (2020). “Extensive heterogeneity in somatic mutation and selection in the human bladder,” Science, 370(6512):75-82.
[cited by applicant]
Lee et al., (2014) “Rare-Variant Association Analysis: Study Designs and Statistical Tests,” Am J Hum Genet., 95(1):5-23.
[cited by applicant]
Lek et al., (2014). “The Challenge of Next Generation Sequencing in the Context of Neuromuscular Diseases,” J Neuromusc Dis, 1(2):135-149.
[cited by applicant]
Levitsky et al., (2021). “Donor-derived cell-free DNA levels predict graft injury in liver transplant recipients,” Am J Transplant, 9 pages.
[cited by applicant]
Levitsky et al., (2021). “Supplemental data: Donor-derived cell-free DNA levels predict graft injury in liver transplant recipients,” Am J Transplant, 2 pages.
[cited by applicant]
Li et al., (2013). “Identifying rare variants associated with complex traits via sequencing,” Curr Protoc Hum Genet., chapter 1, 26 pages.
[cited by applicant]
Li, Hong. et al. Copy number variation in CCL3L1 gene is associated with susceptibility to acute rejection in patients after liver transplantation. Clinical transplantation 26(2):314-321 (2012).
[cited by applicant]
Li, Ying. et al. Ready detection of donor-specific single-nucleotide polymorphisms in the urine of renal transplant recipients by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clinical ch…
[cited by applicant]
Lichtenstein, Anatoly V. et al. Novel applications of polymerase chain reaction to urinary nucleic acid analysis. Clinical Applications of PCR 336:145-154 (2006).
[cited by applicant]
Liu, Jun. et al. Allogeneic CD19-CAR-T cell infusion after allogeneic hematopoietic stem cell transplantation in B cell malignancies. Journal of hematology & oncology 10(1):35, 1-8 (2017).
[cited by applicant]
Liu, Lin et al., Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology. 2012:251364, pp. 1-11 (2012).
[cited by applicant]
Ma, Hao, and Stephen Difazio. An efficient method for purification of PCR products for sequencing. Biotechniques 44(7) :921-923 (2008).
[cited by applicant]
Macaskill, Petra. et al. Assessing the gain in diagnostic performance when combining two diagnostic tests. Statistics in medicine 21(17) :2527-2546 (2002).
[cited by applicant]
Macher et al., (2014). “Monitoring of transplanted liver health by quantification of organ-specific genomic marker in circulating DNA from receptor,” PLoS One, 9(12):e113987, 18 pages.
[cited by applicant]
Mahdi, (2013). “A glow of HLA typing in organ transplantation,” Clin Transl Med., 2(1 ):6, 5 pages.
[cited by applicant]
Mao, Youying. et al. CXCL10 and CXCL13 Expression were highly up-regulated in peripheral blood mononuclear cells in acute rejection and poor response to anti-rejection therapy. Journal of clinical immunology 31(3):414-4…
[cited by applicant]
Marenne et al., (2020). “Exome Sequencing Identifies Genes and Gene Sets Contributing to Severe Childhood Obesity, Linking PHIP Variants to Repressed POMC Transcription,” Cell Metab., 31(6):1107-1119,e1-e12.
[cited by applicant]
Melancon et al., (2020). “Donor-Derived Cell Free DNA: Is It All the Same?” Kidney 360, 1(10):1116-1121.
[cited by applicant]
Merani, Shaheed, and AM James Shapiro. Current status of pancreatic islet transplantation. Clinical science 110(6):611-625 (2006).
[cited by applicant]
Merrill et al., (1955). “Successful homotransplantation of the kidney in an identical twin,” Transactions of the American Clinical and Climatological Association, 67:167-173.
[cited by applicant]
Miotke, Laura. et al. High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR. Analytical chemistry 86(5):2618-2624 (2014).
[cited by applicant]
Mouhieddine et al., (2020). “Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant,” Nat Commun., 11:2996, 9 pages.
[cited by applicant]
Nagano, Y. et al. Development of a genus-specific PCR assay for the molecular detection, confirmation and identification of
[cited by applicant]
Narasimhan et al., (2016). “Health and population effects of rare gene knockouts in adult humans with related parents,” Science, 352(6284):474-477.
[cited by applicant]
Nielsen, Rasmus. et al. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 12(6):443-451 (2011).
[cited by applicant]
North et al., (2020). “Cell-free DNA donor fraction analysis in pediatric and adult heart transplant patients by multiplexed allele-specific quantitative PCR: Validation of a rapid and highly sensitive clinical test for…
[cited by applicant]
Norton et al., (2013). “A stabilizing reagent prevents cell-free DNA contamination by cellular DNA in plasma during blood sample storage and shipping as determined by digital PCR,” Clin Biochem., 46(15):1561-1565.
[cited by applicant]
Oellerich et al., “Donor-derived cell-free DNA as a diagnostic tool in transplantation,” Front. Genet., 13:1031894, (Oct. 2022).
[cited by applicant]
Oeth, Paul et al., Qualitative and Quantitative Genotyping Using Single Base Primer Extension Coupled with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MassARRAY®). Single Nucleotide Pol…
[cited by applicant]
Pakstis, Andrew J. et al., Candidate SNPs for a universal individual identification panel. Hum Genet 121:305-317 (2007).
[cited by applicant]
Pakstis, Andrew J. et al., SNPs for a universal individual identification panel. Hum Genet 127:315-324 (2010).
[cited by applicant]
PCT/US2021/037906 International Search Report and Written Opinion dated Oct. 12, 2021.
[cited by applicant]
Pengelly, (2015). “Genomic data analysis: populations, patients and pipelines,” Dissertation, Univ. of Southampton, available online at https://eprints.soton.ac.uk/397102/, 216 pages.
[cited by applicant]
Pengelly et al., (2013). “A SNP profiling panel for sample tracking in whole-exome sequencing studies,” Genome Med., 5:89, 7 pages.
[cited by applicant]
Pereira, Mariana Buongermino. et al. Comparison of normalization methods for the analysis of metagenomic gene abundance data. BMC genomics 19(1):274, 1-17 (2018).
[cited by applicant]
Pham, Michael X, et al., Gene-expression Profiling for Rejection Surveillance After Cardiac Transplantation. New England Journal of Medicine 362(20):1890-900 (2010).
[cited by applicant]
Price et al., (2006). “Principal components analysis corrects for stratification in genome-wide association studies,” Nature Genetics, 38:904-909.
[cited by applicant]
Purcell et al., (2007). “PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses,” Am J Human Genetics, 81:559-575.
[cited by applicant]
QIAGEN®: QIAamp® Circulating Nucleic Acid Handbook. 64 pages, (2019).
[cited by applicant]
QIAGEN, QIAquick PCR Purification Kit Protocol, Jul. 2008, p. 19-20 (2008).
[cited by applicant]
Quail et al., (2014). “SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing,” BMC Genomics, 15:110, 13 pages.
[cited by applicant]
Quail, Michael et al., A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 13:341, pp. 1-13 (2012).
[cited by applicant]
Riveros-Mckay et al., (2020). “The influence of rare variants in circulating metabolic biomarkers,” PLoS Genet., 16(3):e1008605, 19 pages.
[cited by applicant]
Ro, Han. et al. Association of polymorphisms of interleukin-8, CXCR1, CXCR2, and selectin with allograft outcomes in kidney transplantation. Transplantation 91(1):57-64 (2011).
[cited by applicant]
Roman et al., (2015). “Multiple hepatic regulatory variants at the GALNT2 GWAS locus associated with high-density lipoprotein cholesterol,” Am J Hum Genet., 97(6):801-15.
[cited by applicant]
Saleheen et al., Human knockouts in a cohort with a high rate of consanguinity. bioRxiv, 41 pages (2015).
[cited by applicant]
Samper, Isabelle C. et al. Portable microfluidic biosensing system for real-time analysis of microdialysate in transplant kidneys. Analytical chemistry 91(22):14631-14638 (2019).
[cited by applicant]
Sathirapatya, Tikumphorn et al. A SNP panel for early detection of artificial chimerism in HSCT patients using TaqMan technology. International Journal of Legal Medicine 134(5):1553-1561 (2020).
[cited by applicant]
Saukkonen, Katri et al., Cell-Free Plasma DNA as a Predictor of Outcome in Severe Sepsis and Septic Shock. Clinical Chemistry 54(6):1000-1007 (2008).
[cited by applicant]
Scherer, Andreas. Clinical and ethical considerations of massively parallel sequencing in transplantation science. World Journal of Transplantation 3(4):62-67 (2013).
[cited by applicant]
Schutz, Declaration under 37 CFR §1.132 for U.S. Appl. No. 15/920,356, dated Nov. 16, 2020.
[cited by applicant]
Sehn et al., (2015). “Occult Specimen Contamination in Routine Clinical Next-Generation Sequencing Testing,” Am J Clin Pathol., 144(4):667-674.
[cited by applicant]
Sharon et al., (2017). “Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype,” PLoS Comput Biol., 13(7):e1005629, 19 pages.
[cited by applicant]
Sheldon et al., (2006) “HLA typing and its influence on organ transplantation,” Methods Mo Biol., 333:157-74.
[cited by applicant]