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Kalashnikova E, Aushev VN, Malashevich AK, Tin A, Krinshpun S, Salari R, Scalise CB, Ram R, Malhotra M, Ravi H, Sethi H, Sanchez S, Hagelstrom RT, Brevnov M, Rabinowitz M, Moshkevich S, Zimmermann BG, Liu MC, Aleshin A. Correlation between variant allele frequency and mean tumor molecules with tumor burden in patients with solid tumors. Mol Oncol 2023. [PMID: 38037739 DOI: 10.1002/1878-0261.13557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 10/03/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Several studies have demonstrated the prognostic value of circulating tumor DNA (ctDNA); however, the correlation of mean tumor molecules (MTM)/ml of plasma and mean variant allele frequency (mVAF; %) with clinical parameters is yet to be understood. In this study, we analyzed ctDNA data in a pan-cancer cohort of 23 543 patients who had ctDNA testing performed using a personalized, tumor-informed assay (Signatera™, mPCR-NGS assay). For ctDNA-positive patients, the correlation between MTM/ml and mVAF was examined. Two subanalyses were performed: (a) to establish the association of ctDNA with tumor volume and (b) to assess the correlation between ctDNA dynamics and patient outcomes. On a global cohort, a positive correlation between MTM/ml and mVAF was observed. Among 18 426 patients with longitudinal ctDNA measurements, 13.3% had discordant trajectories between MTM/ml and mVAF at subsequent time points. In metastatic patients receiving immunotherapy (N = 51), changes in ctDNA levels expressed both in MTM/ml and mVAF showed a statistically significant association with progression-free survival; however, the correlation with MTM/ml was numerically stronger.
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Norton ME, MacPherson C, Demko Z, Egbert M, Malone F, Wapner RJ, Roman AS, Khalil A, Faro R, Madankumar R, Strong N, Haeri S, Silver R, Vohra N, Hyett J, Martin K, Rabinowitz M, Jacobsson B, Dar P. Obstetrical, perinatal, and genetic outcomes associated with nonreportable prenatal cell-free DNA screening results. Am J Obstet Gynecol 2023; 229:300.e1-300.e9. [PMID: 36965866 DOI: 10.1016/j.ajog.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023]
Abstract
BACKGROUND The clinical implications of nonreportable cell-free DNA screening results are uncertain, but such results may indicate poor placental implantation in some cases and be associated with adverse obstetrical and perinatal outcomes. OBJECTIVE This study aimed to assess the outcomes of pregnancies with nonreportable cell-free DNA screening in a cohort of patients with complete genetic and obstetrical outcomes. STUDY DESIGN This was a prespecified secondary analysis of a multicenter prospective observational study of prenatal cell-free DNA screening for fetal aneuploidy and 22q11.2 deletion syndrome. Participants who underwent cell-free DNA screening from April 2015 through January 2019 were offered participation. Obstetrical outcomes and neonatal genetic testing results were collected from 21 primary-care and referral centers in the United States, Europe, and Australia. The primary outcome was risk for adverse obstetrical and perinatal outcomes (aneuploidy, preterm birth at <28, <34, and <37 weeks' gestation, preeclampsia, small for gestational age or birthweight <10th percentile for gestational week, and a composite outcome that included preterm birth at <37 weeks, preeclampsia, small for gestational age, and stillbirth at >20 weeks) after nonreportable cell-free DNA screening because of low fetal fraction or other causes. Multivariable analyses were performed, adjusting for variables known to be associated with obstetrical and perinatal outcomes, nonreportable results, or fetal fraction. RESULTS In total, 25,199 pregnant individuals were screened, and 20,194 were enrolled. Genetic confirmation was missing in 1165 (5.8%), 1085 (5.4%) were lost to follow-up, and 93 (0.5%) withdrew; the final study cohort included 17,851 (88.4%) participants who had cell-free DNA, fetal or newborn genetic confirmatory testing, and obstetrical and perinatal outcomes collected. Results were nonreportable in 602 (3.4%) participants. A sample was redrawn and testing attempted again in 427; in 112 (26.2%) participants, results were again nonreportable. Nonreportable results were associated with higher body mass index, chronic hypertension, later gestational age, lower fetal fraction, and Black race. Trisomy 13, 18, or 21 was confirmed in 1.6% with nonreportable tests vs 0.7% with reported results (P=.013). Rates of preterm birth at <28, 34, and 37 weeks, preeclampsia, and the composite outcome were higher among participants with nonreportable results, and further increased among those with a second nonreportable test, whereas the rate of small for gestational age infants was not increased. After adjustment for confounders, the adjusted odds ratios were 2.2 (95% confidence interval, 1.1-4.4) and 2.6 (95% confidence interval, 0.6-10.8) for aneuploidy, and 1.5 (95% confidence interval, 1.2-1.8) and 2.1 (95% confidence interval, 1.4-3.2) for the composite outcome after a first and second nonreportable test, respectively. Of the patients with nonreportable tests, 94.9% had a live birth, as opposed to 98.8% of those with reported test results (adjusted odds ratio for livebirth, 0.20 [95% confidence interval, 0.13-0.30]). CONCLUSION Patients with nonreportable cell-free DNA results are at increased risk for a number of adverse outcomes, including aneuploidy, preeclampsia, and preterm birth. They should be offered diagnostic genetic testing, and clinicians should be aware of the increased risk of pregnancy complications.
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Affiliation(s)
- Mary E Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA.
| | - Cora MacPherson
- Biostatistics Center, George Washington University, Washington, DC
| | | | | | - Fergal Malone
- Department of Obstetrics and Gynaecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia Presbyterian Medical Center, New York, NY
| | - Ashley S Roman
- Department of Obstetrics and Gynecology, New York University Langone Health, New York, NY
| | - Asma Khalil
- Department of Obstetrics and Gynaecology, St George's Hospital, University of London, London, United Kingdom
| | - Revital Faro
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, NJ
| | - Rajeevi Madankumar
- Department of Obstetrics and Gynecology, Long Island Jewish Medical Center, Hyde Park, NY
| | - Noel Strong
- Department of Obstetrics, Gynecology, and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sina Haeri
- Austin Maternal-Fetal Medicine, Austin, TX
| | - Robert Silver
- Department of Obstetrics and Gynecology, The University of Utah, Salt Lake City, UT
| | - Nidhi Vohra
- Department of Obstetrics and Gynecology, North Shore University Hospital, Manhasset, NY
| | - Jon Hyett
- Department of Obstetrics and Gynaecology, Royal Prince Alfred Hospital and Western Sydney University, Sydney, Australia
| | | | | | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pe'er Dar
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY
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Magbanua MJM, Brown Swigart L, Ahmed Z, Sayaman RW, Renner D, Kalashnikova E, Hirst GL, Yau C, Wolf DM, Li W, Delson AL, Asare S, Liu MC, Albain K, Chien AJ, Forero-Torres A, Isaacs C, Nanda R, Tripathy D, Rodriguez A, Sethi H, Aleshin A, Rabinowitz M, Perlmutter J, Symmans WF, Yee D, Hylton NM, Esserman LJ, DeMichele AM, Rugo HS, van 't Veer LJ. Clinical significance and biology of circulating tumor DNA in high-risk early-stage HER2-negative breast cancer receiving neoadjuvant chemotherapy. Cancer Cell 2023; 41:1091-1102.e4. [PMID: 37146605 PMCID: PMC10330514 DOI: 10.1016/j.ccell.2023.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/30/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
Circulating tumor DNA (ctDNA) analysis may improve early-stage breast cancer treatment via non-invasive tumor burden assessment. To investigate subtype-specific differences in the clinical significance and biology of ctDNA shedding, we perform serial personalized ctDNA analysis in hormone receptor (HR)-positive/HER2-negative breast cancer and triple-negative breast cancer (TNBC) patients receiving neoadjuvant chemotherapy (NAC) in the I-SPY2 trial. ctDNA positivity rates before, during, and after NAC are higher in TNBC than in HR-positive/HER2-negative breast cancer patients. Early clearance of ctDNA 3 weeks after treatment initiation predicts a favorable response to NAC in TNBC only. Whereas ctDNA positivity associates with reduced distant recurrence-free survival in both subtypes. Conversely, ctDNA negativity after NAC correlates with improved outcomes, even in patients with extensive residual cancer. Pretreatment tumor mRNA profiling reveals associations between ctDNA shedding and cell cycle and immune-associated signaling. On the basis of these findings, the I-SPY2 trial will prospectively test ctDNA for utility in redirecting therapy to improve response and prognosis.
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Affiliation(s)
| | | | - Ziad Ahmed
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rosalyn W Sayaman
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Gillian L Hirst
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Denise M Wolf
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wen Li
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amy L Delson
- UCSF Breast Science Advocacy Core, San Francisco, CA 94143, USA
| | - Smita Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Minetta C Liu
- Natera, Inc., Austin, TX 78753, USA; Mayo Clinic, Rochester, MN 55905, USA
| | - Kathy Albain
- Loyola University Chicago, Maywood, IL 60153, USA
| | - A Jo Chien
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Rita Nanda
- University of Chicago, Chicago, IL 60637, USA
| | - Debu Tripathy
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | | | | | | | - Jane Perlmutter
- UCSF Breast Science Advocacy Core, San Francisco, CA 94143, USA
| | - W Fraser Symmans
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Douglas Yee
- University of Minnesota, Minneapolis, MN 55455, USA
| | - Nola M Hylton
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J Esserman
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Hope S Rugo
- University of California, San Francisco, San Francisco, CA 94143, USA
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Greer SU, Botello J, Hongo D, Levy B, Shah P, Rabinowitz M, Miller DE, Im K, Kumar A. Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic. J Transl Med 2023; 21:378. [PMID: 37301971 PMCID: PMC10257846 DOI: 10.1186/s12967-023-04243-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Diagnosis of rare genetic diseases can be a long, expensive and complex process, involving an array of tests in the hope of obtaining an actionable result. Long-read sequencing platforms offer the opportunity to make definitive molecular diagnoses using a single assay capable of detecting variants, characterizing methylation patterns, resolving complex rearrangements, and assigning findings to long-range haplotypes. Here, we demonstrate the clinical utility of Nanopore long-read sequencing by validating a confirmatory test for copy number variants (CNVs) in neurodevelopmental disorders and illustrate the broader applications of this platform to assess genomic features with significant clinical implications. METHODS We used adaptive sampling on the Oxford Nanopore platform to sequence 25 genomic DNA samples and 5 blood samples collected from patients with known or false-positive copy number changes originally detected using short-read sequencing. Across the 30 samples (a total of 50 with replicates), we assayed 35 known unique CNVs (a total of 55 with replicates) and one false-positive CNV, ranging in size from 40 kb to 155 Mb, and assessed the presence or absence of suspected CNVs using normalized read depth. RESULTS Across 50 samples (including replicates) sequenced on individual MinION flow cells, we achieved an average on-target mean depth of 9.5X and an average on-target read length of 4805 bp. Using a custom read depth-based analysis, we successfully confirmed the presence of all 55 known CNVs (including replicates) and the absence of one false-positive CNV. Using the same CNV-targeted data, we compared genotypes of single nucleotide variant loci to verify that no sample mix-ups occurred between assays. For one case, we also used methylation detection and phasing to investigate the parental origin of a 15q11.2-q13 duplication with implications for clinical prognosis. CONCLUSIONS We present an assay that efficiently targets genomic regions to confirm clinically relevant CNVs with a concordance rate of 100%. Furthermore, we demonstrate how integration of genotype, methylation, and phasing data from the Nanopore sequencing platform can potentially simplify and shorten the diagnostic odyssey.
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Affiliation(s)
| | | | - Donna Hongo
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
| | - Brynn Levy
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Premal Shah
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
| | - Matthew Rabinowitz
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
- Natera Inc., San Carlos, CA, USA
| | - Danny E Miller
- Department of Pediatrics, Department of Laboratory Medicine and Pathology, University of Washington, WA, Seattle, USA
| | - Kate Im
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA
| | - Akash Kumar
- MyOme Inc., 535 Middlefield Rd Suite 170, Menlo Park, CA, USA.
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Griggs-Demmin A, Rabinowitz M, Paul A, Herati A. Remote spinal trauma resulting in dorsal column spinal pathway dysfunction and anejaculation. Urol Case Rep 2023; 47:102323. [PMID: 36895468 PMCID: PMC9988461 DOI: 10.1016/j.eucr.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 02/12/2023] Open
Abstract
Spinal cord injury (SCI) as the cause of anejaculation is a rare entity. We present the case of a 65-year-old male with a five-year history of intractable anejaculation. Two years prior to onset of his anejaculation, the patient fell from height, causing minor spinal trauma, with sequelae of cervical myelopathy and eventual posterior spinal fusion of C1/C2. Biothesiometry and sensory evaluation revealed diminished somatic sensation of his glans penis in a frequency-dependent pattern. The patient's pudendal sensory loss and anejaculation correlate with his spinal trauma, as evidenced by the lack of peripheral nervous system findings upon neurological exam and imaging.
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Affiliation(s)
| | - Matthew Rabinowitz
- Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Ashley Paul
- Parkinson's Disease and Movement Disorders Center, Johns Hopkins Outpatient Center, 601 N. Caroline St., Baltimore, MD, 21287, USA
| | - Amin Herati
- Brady Urological Institute, Johns Hopkins Medicine, 600 N. Wolfe St., Baltimore, MD, 21287
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6
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Brancati F, Fredericks PJ, Rabinowitz M, Liu J, Solomon A, Cohen A. Conservative management of scrotal pyoceles - A case series and literature review. Am J Emerg Med 2023; 67:48-50. [PMID: 36804748 DOI: 10.1016/j.ajem.2023.01.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/08/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
STUDY OBJECTIVE We describe the common presenting signs and symptoms, treatment modalities, and outcomes of acutely presenting scrotal pyoceles. METHODS We conducted a retrospective chart review of all adult patients treated for ultrasound-confirmed scrotal pyoceles between 2010 and 2020 at two sites within the [redacted]. Vitals at presentation, microbiology, and inpatient courses including antibiotic treatment and surgical procedures were collected. RESULTS A total of 360 scrotal ultrasounds were reviewed identifying 15 patients with pyoceles, 11 patients presenting to the emergency department and 4 hospitalized patients. The most common chief complaint was testicular pain (67%). Only seven patients (47%) met SIRS criteria upon presentation. All patients were initially treated with broad-spectrum antibiotics and observation; 11 (73%) responded to this management alone, while four patients (27%) required surgical drainage due to persistent infection. No patients contracted Fournier's gangrene. CONCLUSION This study reports the largest published database of scrotal pyoceles to date and describes our clinical approach to management. While pyoceles have traditionally been treated aggressively with surgical drainage, this case series suggests that most patients improve with broad-spectrum antibiotic treatment and observation alone, requiring surgical drainage if infection persists. Future investigations including multi-institutional data will be necessary to validate our institution's approach.
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Affiliation(s)
- Francesca Brancati
- The Johns Hopkins University School of Medicine, 733 N Broadway St., Baltimore, MD 21205, USA.
| | - Peter James Fredericks
- Department of Emergency Medicine, The Johns Hopkins Hospital, 1800 Orleans Street Sheikh Zayed 1, Room 1085, Baltimore, MD 21287, USA.
| | - Matthew Rabinowitz
- The Johns Hopkins University School of Medicine, 733 N Broadway St., Baltimore, MD 21205, USA.
| | - James Liu
- Department of Urology, The Johns Hopkins Hospital, 600 N Wolfe St., Baltimore, MD 21287, USA.
| | - Alex Solomon
- Department of Radiology, The Johns Hopkins Hospital, 601 N Caroline St., Baltimore, MD 21287, USA.
| | - Andrew Cohen
- The Brady Urological Institute and Department of Urology, The Johns Hopkins Hospital, 600 N Wolfe St, Baltimore, MD 21287, USA.
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Tshiaba PT, Ratman DK, Sun JM, Tunstall TS, Levy B, Shah PS, Weitzel JN, Rabinowitz M, Kumar A, Im KM. Integration of a Cross-Ancestry Polygenic Model With Clinical Risk Factors Improves Breast Cancer Risk Stratification. JCO Precis Oncol 2023; 7:e2200447. [PMID: 36809055 DOI: 10.1200/po.22.00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
PURPOSE To develop and validate a cross-ancestry integrated risk score (caIRS) that combines a cross-ancestry polygenic risk score (caPRS) with a clinical estimator for breast cancer (BC) risk. We hypothesized that the caIRS is a better predictor of BC risk than clinical risk factors across diverse ancestry groups. METHODS We used diverse retrospective cohort data with longitudinal follow-up to develop a caPRS and integrate it with the Tyrer-Cuzick (T-C) clinical model. We tested the association between the caIRS and BC risk in two validation cohorts including > 130,000 women. We compared model discrimination for 5-year and remaining lifetime BC risk between the caIRS and T-C and assessed how the caIRS would affect screening in the clinic. RESULTS The caIRS outperformed T-C alone for all populations tested in both validation cohorts and contributed significantly to risk prediction beyond T-C. The area under the receiver operating characteristic curve improved from 0.57 to 0.65, and the odds ratio per standard deviation increased from 1.35 (95% CI, 1.27 to 1.43) to 1.79 (95% CI, 1.70 to 1.88) in validation cohort 1 with similar improvements observed in validation cohort 2. We observed the largest gain in positive predictive value using the caIRS in Black/African American women across both validation cohorts, with an approximately two-fold increase and an equivalent negative predictive value as the T-C. In a multivariate, age-adjusted logistic regression model including both caIRS and T-C, caIRS remained significant, indicating that caIRS provides information over T-C alone. CONCLUSION Adding a caPRS to the T-C model improves BC risk stratification for women of multiple ancestries, which could have implications for screening recommendations and prevention.
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Affiliation(s)
| | | | | | | | - Brynn Levy
- MyOme Inc, Menlo Park, CA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
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Srinivasan P, Gutman B, Aushev V, Sharma S, Arbel T, Wu HT, Malhotra M, Salari R, Zimmermann B, Swenerton R, Kawli T, Mitchell B, Rabinowitz M, Aleshin A, Reiter JG. Abstract P040: Mutational heterogeneity of colorectal cancers across ancestries and its implications for cancer early detection. Cancer Prev Res (Phila) 2023. [DOI: 10.1158/1940-6215.precprev22-p040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Abstract
Introduction: Early cancer detection with liquid biopsies has the potential to reduce mortality rates by improving screening strategies, adoption, and adherence. Towards this, a deeper understanding of the cancer genomic landscape among patients of different ethnicities is critical to ensure comparable performance across a broad population. In this study, we sought to understand how the mutational landscape of patients with colorectal cancer (CRC) varies across ethnicities. Methods: A total of 20,845 de-identified patients with stage I-IV CRC, who had undergone commercial personalized and tumor-informed ctDNA testing (SignateraTM) as of April 14, 2022, were eligible for inclusion in the study. We performed ancestry inference using Principal Component Analysis on single nucleotide polymorphisms (SNPs) and validated the predictions in a subset of 2,032 patients with whole exome sequencing data available along with self-reported ethnicity. Individuals were assigned to one of four major ethnic groups: African (AFR), European (EUR), East Asian (EAS) and South Asian (SAS). Results: Our cohort consisted of 69.1% EUR, 9.6% AFR, 20% EAS, and 1.3% SAS patients. On comparing the somatic driver mutations across ancestry groups, we observed APC mutations in 71% of EUR, 79% of AFR, 80% of EAS and 69% of SAS (p<0.0001), KRAS mutations in 39% of EUR, 50% of AFR, 40% of EAS and 38% of SAS (p<0.0001), and TP53 mutations in 64% in EUR, 64% in AFR, 74% in EAS and 69% in SAS (p<0.0001) patients, respectively. The microsatellite instability (MSI) rates similarly varied across ancestral groups, with EUR ancestry (12.3%) having a significantly higher rate of MSI than AFR (8.9%) and EAS (7.5%) (p<0.0001). Comparing the mutational patterns in left vs. right colon across 712 patients with available tumor location information, we found 64% of tumors in EAS to be left sided vs. 49% in EUR (p=0.0002). Left-sided tumors were enriched for MSI and RAS mutations and right-sided tumors were enriched for APC and TP53 mutations, confirming known differences in left- vs. right-sided colorectal tumors. Among left sided tumors, we also observed TP53 mutations in 79% of EAS as compared to 64% of EUR (p=0.001), APC mutations in 84% of EAS as compared to 70% of EUR (p=0.002) and RNF43 mutations in 1% of EAS as compared to 7% in EUR (p=0.002) suggesting differences in mechanisms of WNT pathway inactivation across ethnicities. Finally, we looked at the predicted performance of a cancer screening panel which is based on large and heterogeneous data and maximizes recurrent mutation coverage while minimizing panel size. Despite the differences in individual driver gene mutation frequency, we found that the mean number of mutations covered by the panel in AFR, EAS and SAS individuals relative to EUR was 1.07, 1.1 and 1.02, respectively. Conclusions: Our results demonstrate that the expected performance of a theoretical cancer screening panel was similar across the different ancestry groups despite differences in their somatic landscape.
Citation Format: Preethi Srinivasan, Boris Gutman, Vasily Aushev, Shruti Sharma, Taly Arbel, Hsin-Ta Wu, Meenakshi Malhotra, Raheleh Salari, Bernhard Zimmermann, Ryan Swenerton, Trupti Kawli, Breeana Mitchell, Matthew Rabinowitz, Alexey Aleshin, Johannes G. Reiter. Mutational heterogeneity of colorectal cancers across ancestries and its implications for cancer early detection. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P040.
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Halloran PF, Reeve J, Madill-Thomsen KS, Kaur N, Ahmed E, Cantos C, Al Haj Baddar N, Demko Z, Liang N, Swenerton RK, Zimmermann BG, Van Hummelen P, Prewett A, Rabinowitz M, Tabriziani H, Gauthier P, Billings P. Combining Donor-derived Cell-free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology as Confirmation. Transplantation 2022; 106:2435-2442. [PMID: 35765145 PMCID: PMC9698190 DOI: 10.1097/tp.0000000000004212] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/14/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Donor-derived cell-free DNA (dd-cfDNA) fraction and quantity have both been shown to be associated with allograft rejection. The present study compared the relative predictive power of each of these variables to the combination of the two, and developed an algorithm incorporating both variables to detect active rejection in renal allograft biopsies. METHODS The first 426 sequential indication biopsy samples collected from the Trifecta study ( ClinicalTrials.gov # NCT04239703) with microarray-derived gene expression and dd-cfDNA results were included. After exclusions to simulate intended clinical use, 367 samples were analyzed. Biopsies were assessed using the molecular microscope diagnostic system and histology (Banff 2019). Logistic regression analysis examined whether combining dd-cfDNA fraction and quantity adds predictive value to either alone. The first 149 sequential samples were used to develop a two-threshold algorithm and the next 218 to validate the algorithm. RESULTS In regression, the combination of dd-cfDNA fraction and quantity was found to be significantly more predictive than either variable alone ( P = 0.009 and P < 0.0001). In the test set, the area under the receiver operating characteristic curve of the two-variable system was 0.88, and performance of the two-threshold algorithm showed a sensitivity of 83.1% and specificity of 81.0% for molecular diagnoses and a sensitivity of 73.5% and specificity of 80.8% for histology diagnoses. CONCLUSIONS This prospective, biopsy-matched, multisite dd-cfDNA study in kidney transplant patients found that the combination of dd-cfDNA fraction and quantity was more powerful than either dd-cfDNA fraction or quantity alone and validated a novel two-threshold algorithm incorporating both variables.
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Affiliation(s)
- Philip F. Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | - Jeff Reeve
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - the Trifecta Investigators*
- Alberta Transplant Applied Genomics Centre, Edmonton, University of Alberta, Canada
- Natera Inc, San Carlos, CA
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Tshiaba P, Sun J, Ratman D, Tunstall T, Levy B, Shah P, Rabinowitz M, Kumar A, Im K. Cross-ancestry polygenic risk score for breast cancer risk assessment. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.10540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
10540 Background: Breast cancer (BC) risk is influenced by many common variants with small effects. Polygenic risk scores (PRS) weight these variants based on genome-wide association studies (GWAS) and aggregate them into a single measure. PRS has primarily shown benefit in Caucasian women. We established a cross-ancestry polygenic model (caPRS) which assesses risk of breast cancer across multiple ancestries. Methods: Performance of multiple BC polygenic models, both published and developed in-house, were evaluated for each of five ancestry groups: European, African, South Asian, East Asian, and Admixed American. To account for ancestry-specific mean and variance, we computed principal components (PCs) for all women by projecting their genotypes onto PCs calculated on individuals in the 1000 Genomes Project (1KGP). We next centered each ancestry-specific PRS by subtracting the PRS predicted from a linear regression of PRS against the first four PCs in unaffected individuals. Each centered PRS was then divided by the SD of the corresponding 1KGP population. We defined a cross-ancestry polygenic model as a linear combination of the best performing PRS model for each ancestry group weighted by fractional ancestry. Association of the caPRS with breast cancer risk was tested in a validation cohort of >130,000 women consisting of multiple independent cohorts (the Women’s Health Initiative, the Multiethnic Cohort, the ROOT cohort and the UK Biobank) using a multivariate logistic regression model that included caPRS, age, self-reported ancestry, personal history of ovarian cancer (when available) and first-degree family history of BC. Discrimination was assessed by the odds ratio (OR) per SD and the area under the receiver-operator curve (AUC). Results: This study included women with African/Black, East Asian, Caucasian/White, Hispanic/Latino, South Asian and ‘Other’ self-reported ancestry. The ancestry-specific models included in the caPRS ranged in size from 173 to >800,000 variants. The caPRS was associated with BC risk for women in each self-reported ancestry (Table). The caPRS offered a modest increase in performance over a commonly implemented 313-SNP PRS in non-European ancestries, most significantly in African/Black women where the OR per SD increased from 1.24 (1.08 - 1.43), p-value 2.3x10-3. Conclusions: The caPRS performed well for women of any ancestry and allows flexibility to update ancestry-specific models. These results suggest the caPRS has the potential to improve the clinical utility of existing clinical risk predictors. [Table: see text]
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11
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Rabinowitz M, Bowring MG, Kohn T, Levy J, Herati A. Impact of Environmental and Socioeconomic Factors on Semen Quality in the United States. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.01.235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Kumar A, Im K, Banjevic M, Ng PC, Tunstall T, Garcia G, Galhardo L, Sun J, Schaedel ON, Levy B, Hongo D, Kijacic D, Kiehl M, Tran ND, Klatsky PC, Rabinowitz M. Whole-genome risk prediction of common diseases in human preimplantation embryos. Nat Med 2022; 28:513-516. [PMID: 35314819 PMCID: PMC8938270 DOI: 10.1038/s41591-022-01735-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/04/2022] [Indexed: 12/14/2022]
Abstract
Preimplantation genetic testing (PGT) of in-vitro-fertilized embryos has been proposed as a method to reduce transmission of common disease; however, more comprehensive embryo genetic assessment, combining the effects of common variants and rare variants, remains unavailable. Here, we used a combination of molecular and statistical techniques to reliably infer inherited genome sequence in 110 embryos and model susceptibility across 12 common conditions. We observed a genotype accuracy of 99.0–99.4% at sites relevant to polygenic risk scoring in cases from day-5 embryo biopsies and 97.2–99.1% in cases from day-3 embryo biopsies. Combining rare variants with polygenic risk score (PRS) magnifies predicted differences across sibling embryos. For example, in a couple with a pathogenic BRCA1 variant, we predicted a 15-fold difference in odds ratio (OR) across siblings when combining versus a 4.5-fold or 3-fold difference with BRCA1 or PRS alone. Our findings may inform the discussion of utility and implementation of genome-based PGT in clinical practice. A computational approach combining whole-genome sequencing of parental genomes and genotyping of preimplantation embryos allows accurate prediction of the inherited genomes of embryos and calculation of polygenic risk scores.
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Affiliation(s)
| | - Kate Im
- MyOme, Inc., Menlo Park, CA, USA
| | | | | | | | | | | | | | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | - Nam D Tran
- Spring Fertility, San Francisco, CA, USA
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13
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Dar P, Jacobsson B, MacPherson C, Egbert M, Malone F, Wapner RJ, Roman AS, Khalil A, Faro R, Madankumar R, Edwards L, Haeri S, Silver R, Vohra N, Hyett J, Clunie G, Demko Z, Martin K, Rabinowitz M, Flood K, Carlsson Y, Doulaveris G, Malone C, Hallingstrom M, Klugman S, Clifton R, Kao C, Hakonarson H, Norton ME. Cell-free DNA screening for trisomies 21, 18, and 13 in pregnancies at low and high risk for aneuploidy with genetic confirmation. Am J Obstet Gynecol 2022; 227:259.e1-259.e14. [PMID: 35085538 DOI: 10.1016/j.ajog.2022.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Cell-free DNA noninvasive prenatal screening for trisomies 21, 18, and 13 has been rapidly adopted into clinical practice. However, previous studies are limited by a lack of follow-up genetic testing to confirm the outcomes and accurately assess test performance, particularly in women at a low risk for aneuploidy. OBJECTIVE To measure and compare the performance of cell-free DNA screening for trisomies 21, 18, and 13 between women at a low and high risk for aneuploidy in a large, prospective cohort with genetic confirmation of results STUDY DESIGN: This was a multicenter prospective observational study at 21 centers in 6 countries. Women who had single-nucleotide-polymorphism-based cell-free DNA screening for trisomies 21, 18, and 13 were enrolled. Genetic confirmation was obtained from prenatal or newborn DNA samples. The test performance and test failure (no-call) rates were assessed for the cohort, and women with low and high previous risks for aneuploidy were compared. An updated cell-free DNA algorithm blinded to the pregnancy outcome was also assessed. RESULTS A total of 20,194 women were enrolled at a median gestational age of 12.6 weeks (interquartile range, 11.6-13.9). The genetic outcomes were confirmed in 17,851 cases (88.4%): 13,043 (73.1%) low-risk and 4808 (26.9%) high-risk cases for aneuploidy. Overall, 133 trisomies were diagnosed (100 trisomy 21; 18 trisomy 18; 15 trisomy 13). The cell-free DNA screen positive rate was lower in the low-risk vs the high-risk group (0.27% vs 2.2%; P<.0001). The sensitivity and specificity were similar between the groups. The positive predictive value for the low- and high-risk groups was 85.7% vs 97.5%; P=.058 for trisomy 21; 50.0% vs 81.3%; P=.283 for trisomy 18; and 62.5% vs 83.3; P=.58 for trisomy 13, respectively. Overall, 602 (3.4%) patients had no-call result after the first draw and 287 (1.61%) after including cases with a second draw. The trisomy rate was higher in the 287 cases with no-call results than patients with a result on a first draw (2.8% vs 0.7%; P=.001). The updated algorithm showed similar sensitivity and specificity to the study algorithm with a lower no-call rate. CONCLUSION In women at a low risk for aneuploidy, single-nucleotide-polymorphism-based cell-free DNA has high sensitivity and specificity, positive predictive value of 85.7% for trisomy 21 and 74.3% for the 3 common trisomies. Patients who receive a no-call result are at an increased risk of aneuploidy and require additional investigation.
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Affiliation(s)
- Pe'er Dar
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY.
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Cora MacPherson
- The Biostatistics Center, George Washington University, Washington, DC
| | | | - Fergal Malone
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Ashley S Roman
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY
| | - Asma Khalil
- Department of Obstetrics and Gynecology, St George's Hospital, University of London, London, United Kingdom
| | - Revital Faro
- Department of Obstetrics and Gynecology, St. Peter's University Hospital, New Brunswick, NJ
| | - Rajeevi Madankumar
- Department of Obstetrics and Gynecology, Long Island Jewish Medical Center, Hyde Park, NY
| | | | - Sina Haeri
- Austin Maternal-Fetal Medicine, Austin, TX
| | - Robert Silver
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT
| | - Nidhi Vohra
- Department of Obstetrics and Gynecology, North Shore University Hospital, Manhasset, NY
| | - Jon Hyett
- Department of Obstetrics and Gynecology, Royal Prince Alfred Hospital, University of Sydney, Camperdown, Australia
| | - Garfield Clunie
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Karen Flood
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ylva Carlsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Georgios Doulaveris
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY
| | - Ciara Malone
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maria Hallingstrom
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Susan Klugman
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY
| | - Rebecca Clifton
- The Biostatistics Center, George Washington University, Washington, DC
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mary E Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA
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Dar P, Jacobsson B, Clifton R, Egbert M, Malone F, Wapner RJ, Roman AS, Khalil A, Faro R, Madankumar R, Edwards L, Strong N, Haeri S, Silver R, Vohra N, Hyett J, Demko Z, Martin K, Rabinowitz M, Flood K, Carlsson Y, Doulaveris G, Daly S, Hallingström M, MacPherson C, Kao C, Hakonarson H, Norton ME. Cell-free DNA screening for prenatal detection of 22q11.2 deletion syndrome. Am J Obstet Gynecol 2022; 227:79.e1-79.e11. [PMID: 35033576 DOI: 10.1016/j.ajog.2022.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Historically, prenatal screening has focused primarily on the detection of fetal aneuploidies. Cell-free DNA now enables noninvasive screening for subchromosomal copy number variants, including 22q11.2 deletion syndrome (or DiGeorge syndrome), which is the most common microdeletion and a leading cause of congenital heart defects and neurodevelopmental delay. Although smaller studies have demonstrated the feasibility of screening for 22q11.2 deletion syndrome, large cohort studies with confirmatory postnatal testing to assess test performance have not been reported. OBJECTIVE This study aimed to assess the performance of single-nucleotide polymorphism-based, prenatal cell-free DNA screening for detection of 22q11.2 deletion syndrome. STUDY DESIGN Patients who underwent single-nucleotide polymorphism-based prenatal cell-free DNA screening for 22q11.2 deletion syndrome were prospectively enrolled at 21 centers in 6 countries. Prenatal or newborn DNA samples were requested in all cases for genetic confirmation using chromosomal microarrays. The primary outcome was sensitivity, specificity, positive predictive value, and negative predictive value of cell-free DNA screening for the detection of all deletions, including the classical deletion and nested deletions that are ≥500 kb, in the 22q11.2 low-copy repeat A-D region. Secondary outcomes included the prevalence of 22q11.2 deletion syndrome and performance of an updated cell-free DNA algorithm that was evaluated with blinding to the pregnancy outcome. RESULTS Of the 20,887 women enrolled, a genetic outcome was available for 18,289 (87.6%). A total of 12 22q11.2 deletion syndrome cases were confirmed in the cohort, including 5 (41.7%) nested deletions, yielding a prevalence of 1 in 1524. In the total cohort, cell-free DNA screening identified 17,976 (98.3%) cases as low risk for 22q11.2 deletion syndrome and 38 (0.2%) cases as high risk; 275 (1.5%) cases were nonreportable. Overall, 9 of 12 cases of 22q11.2 were detected, yielding a sensitivity of 75.0% (95% confidence interval, 42.8-94.5); specificity of 99.84% (95% confidence interval, 99.77-99.89); positive predictive value of 23.7% (95% confidence interval, 11.44-40.24), and negative predictive value of 99.98% (95% confidence interval, 99.95-100). None of the cases with a nonreportable result was diagnosed with 22q11.2 deletion syndrome. The updated algorithm detected 10 of 12 cases (83.3%; 95% confidence interval, 51.6-97.9) with a lower false positive rate (0.05% vs 0.16%; P<.001) and a positive predictive value of 52.6% (10/19; 95% confidence interval, 28.9-75.6). CONCLUSION Noninvasive cell-free DNA prenatal screening for 22q11.2 deletion syndrome can detect most affected cases, including smaller nested deletions, with a low false positive rate.
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Affiliation(s)
- Pe'er Dar
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY.
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rebecca Clifton
- The Biostatistics Center, George Washington University, Rockville, MD
| | | | - Fergal Malone
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Ashley S Roman
- Department of Obstetrics and Gynecology, New York University Langone, New York, NY
| | - Asma Khalil
- Department of Obstetrics and Gynaecology, St George's Hospital, University of London, London, United Kingdom
| | - Revital Faro
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, NJ
| | - Rajeevi Madankumar
- Department of Obstetrics and Gynecology, Long Island Jewish Medical Center, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY
| | | | - Noel Strong
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sina Haeri
- Austin Maternal-Fetal Medicine, Austin, TX
| | - Robert Silver
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT
| | - Nidhi Vohra
- Department of Obstetrics and Gynecology, North Shore University Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Jon Hyett
- Department of Obstetrics and Gynecology, Royal Prince Alfred Hospital, University of Sydney, Camperdown, New South Wales, Australia
| | | | | | | | - Karen Flood
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ylva Carlsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Georgios Doulaveris
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY
| | - Sean Daly
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maria Hallingström
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Cora MacPherson
- The Biostatistics Center, George Washington University, Rockville, MD
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mary E Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
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Miyo M, Kato T, Nakamura Y, Taniguchi H, Takahashi Y, Ishii M, Okita K, Ando K, Yukami H, Mishima S, Yamazaki K, Kotaka M, Watanabe J, Oba K, Aleshin A, Billings PR, Rabinowitz M, Kotani D, Oki E, Takemasa I, Mori M, Yoshino T. DENEB: Development of new criteria for curability after local excision of pathological T1 colorectal cancer using liquid biopsy. Cancer Sci 2021; 113:1531-1534. [PMID: 34839585 PMCID: PMC8990725 DOI: 10.1111/cas.15226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/13/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
According to the current international guidelines, high‐risk patients diagnosed with pathological T1 (pT1) colorectal cancer (CRC) who underwent complete local resection but may have risk of developing lymph node metastasis (LNM) are recommended additional intestinal resection with lymph node dissection. However, around 90% of the patients without LNM are exposed to the risk of being overtreated due to the insufficient pathological criteria for risk stratification of LNM. Circulating tumor DNA (ctDNA) is a noninvasive biomarker for molecular residual disease and relapse detection after treatments including surgical and endoscopic resection of solid tumors. The CIRCULATE‐Japan project includes a large‐scale patient‐screening registry of the GALAXY study to track ctDNA status of patients with stage II to IV or recurrent CRC that can be completely resected. Based on the CIRCULATE‐Japan platform, we launched DENEB, a new prospective study, within the GALAXY study for patients with pT1 CRC who underwent complete local resection and were scheduled for additional intestinal resection with lymph node dissection based on the standard pathologic risk stratification criteria for LNM. The aim of this study is to explore the ability of predicting LNM using ctDNA analysis compared with the standard pathological criteria. The ctDNA assay will build new evidence to establish a noninvasive personalized diagnosis in patients, which will facilitate tailored/optimal treatment strategies for CRC patients.
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Affiliation(s)
- Masaaki Miyo
- Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Takeshi Kato
- Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroya Taniguchi
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yusuke Takahashi
- Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Masayuki Ishii
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Kenji Okita
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Koji Ando
- Department of Surgery and Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - Hiroki Yukami
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Saori Mishima
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | | | - Jun Watanabe
- Department of Surgery, Gastroenterological Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Koji Oba
- Interfaculty Initiative in Information Studies, The University of Tokyo, Tokyo, Japan
| | | | | | | | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - Ichiro Takemasa
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Masaki Mori
- Tokai University School of Medicine, Isehara, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
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16
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17
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Taniguchi H, Nakamura Y, Kotani D, Yukami H, Mishima S, Sawada K, Shirasu H, Ebi H, Yamanaka T, Aleshin A, Billings PR, Rabinowitz M, Oki E, Takemasa I, Kato T, Mori M, Yoshino T. CIRCULATE-Japan: Circulating tumor DNA-guided adaptive platform trials to refine adjuvant therapy for colorectal cancer. Cancer Sci 2021; 112:2915-2920. [PMID: 33931919 PMCID: PMC8253296 DOI: 10.1111/cas.14926] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/13/2021] [Indexed: 12/14/2022] Open
Abstract
Adjuvant chemotherapy has reduced the risk of tumor recurrence and improved survival in patients with resected colorectal cancer. Potential utility of circulating tumor DNA (ctDNA) prior to and post surgery has been reported across various solid tumors. We initiated a new type of adaptive platform trials to evaluate the clinical benefits of ctDNA analysis and refine precision adjuvant therapy for resectable colorectal cancer, named CIRCULATE‐Japan including three clinical trials. The GALAXY study is a prospectively conducted large‐scale registry designed to monitor ctDNA for patients with clinical stage II to IV or recurrent colorectal cancer who can undergo complete surgical resection. The VEGA trial is a randomized phase III study designed to test whether postoperative surgery alone is noninferior to the standard therapy with capecitabine plus oxaliplatin for 3 months in patients with high‐risk stage II or low‐risk stage III colon cancer if ctDNA status is negative at week 4 after curative surgery in the GALAXY study. The ALTAIR trial is a double‐blind, phase III study designed to establish the superiority of trifluridine/tipiracil as compared with placebo in patients with resected colorectal cancer who show circulating tumor–positive status in the GALAXY study. Therefore, CIRCULATE‐Japan encompasses both “de‐escalation” and “escalation” trials for ctDNA‐negative and ‐positive patients, respectively, and helps to answer whether measuring ctDNA postoperatively has prognostic and/or predictive value. Our ctDNA‐guided adaptive platform trials will accelerate clinical development toward further precision oncology in the field of adjuvant therapy. Analysis of ctDNA status could be utilized as a predictor of risk stratification for recurrence and to monitor the effectiveness of adjuvant chemotherapy. ctDNA is a promising, noninvasive tumor biomarker that can aid in tumor monitoring throughout disease management.
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Affiliation(s)
- Hiroya Taniguchi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan.,Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan.,Translational Research Support Section, National Cancer Center Hospital East, Kashiwa, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroki Yukami
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Saori Mishima
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kentaro Sawada
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiromichi Shirasu
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Sunto-gun, Japan
| | - Hiromichi Ebi
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takeharu Yamanaka
- Department of Biostatistics, National Cancer Center Hospital East, Kashiwa, Japan
| | | | | | | | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ichiro Takemasa
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Takeshi Kato
- Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Masaki Mori
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Tokai University School of Medicine, Isehara, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
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Rabinowitz M, Alam R, Liu J, Kohn T, Peña V, Herati A. 023 Evaluating the Impact of Telemedicine on Access to Male Sexual Medicine During the COVID-era. J Sex Med 2021. [DOI: 10.1016/j.jsxm.2021.01.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Westemeyer M, Saucier J, Wallace J, Prins SA, Shetty A, Malhotra M, Demko ZP, Eng CM, Weckstein L, Boostanfar R, Rabinowitz M, Benn P, Keen-Kim D, Billings P. Correction: Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach. Genet Med 2020; 22:1282. [PMID: 32483296 PMCID: PMC7332416 DOI: 10.1038/s41436-020-0853-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Reinert T, Henriksen TV, Christensen E, Sharma S, Salari R, Sethi H, Knudsen M, Nordentoft I, Wu HT, Tin AS, Heilskov Rasmussen M, Vang S, Shchegrova S, Frydendahl Boll Johansen A, Srinivasan R, Assaf Z, Balcioglu M, Olson A, Dashner S, Hafez D, Navarro S, Goel S, Rabinowitz M, Billings P, Sigurjonsson S, Dyrskjøt L, Swenerton R, Aleshin A, Laurberg S, Husted Madsen A, Kannerup AS, Stribolt K, Palmelund Krag S, Iversen LH, Gotschalck Sunesen K, Lin CHJ, Zimmermann BG, Lindbjerg Andersen C. Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer. JAMA Oncol 2019; 5:1124-1131. [PMID: 31070691 PMCID: PMC6512280 DOI: 10.1001/jamaoncol.2019.0528] [Citation(s) in RCA: 466] [Impact Index Per Article: 93.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Importance Novel sensitive methods for detection and monitoring of residual disease can improve postoperative risk stratification with implications for patient selection for adjuvant chemotherapy (ACT), ACT duration, intensity of radiologic surveillance, and, ultimately, outcome for patients with colorectal cancer (CRC). Objective To investigate the association of circulating tumor DNA (ctDNA) with recurrence using longitudinal data from ultradeep sequencing of plasma cell-free DNA in patients with CRC before and after surgery, during and after ACT, and during surveillance. Design, Setting, and Participants In this prospective, multicenter cohort study, ctDNA was quantified in the preoperative and postoperative settings of stages I to III CRC by personalized multiplex, polymerase chain reaction-based, next-generation sequencing. The study enrolled 130 patients at the surgical departments of Aarhus University Hospital, Randers Hospital, and Herning Hospital in Denmark from May 1, 2014, to January 31, 2017. Plasma samples (n = 829) were collected before surgery, postoperatively at day 30, and every third month for up to 3 years. Main Outcomes and Measures Outcomes were ctDNA measurement, clinical recurrence, and recurrence-free survival. Results A total of 130 patients with stages I to III CRC (mean [SD] age, 67.9 [10.1] years; 74 [56.9%] male) were enrolled in the study; 5 patients discontinued participation, leaving 125 patients for analysis. Preoperatively, ctDNA was detectable in 108 of 122 patients (88.5%). After definitive treatment, longitudinal ctDNA analysis identified 14 of 16 relapses (87.5%). At postoperative day 30, ctDNA-positive patients were 7 times more likely to relapse than ctDNA-negative patients (hazard ratio [HR], 7.2; 95% CI, 2.7-19.0; P < .001). Similarly, shortly after ACT ctDNA-positive patients were 17 times (HR, 17.5; 95% CI, 5.4-56.5; P < .001) more likely to relapse. All 7 patients who were ctDNA positive after ACT experienced relapse. Monitoring during and after ACT indicated that 3 of the 10 ctDNA-positive patients (30.0%) were cleared by ACT. During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA-negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Serial ctDNA analyses revealed disease recurrence up to 16.5 months ahead of standard-of-care radiologic imaging (mean, 8.7 months; range, 0.8-16.5 months). Actionable mutations were identified in 81.8% of the ctDNA-positive relapse samples. Conclusions and Relevance Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection.
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Affiliation(s)
- Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Søren Laurberg
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Katrine Stribolt
- Department of Pathology, Regional Hospital Randers, Randers, Denmark
| | | | - Lene H Iversen
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
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21
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Christensen E, Birkenkamp-Demtröder K, Sethi H, Shchegrova S, Salari R, Nordentoft I, Wu HT, Knudsen M, Lamy P, Lindskrog SV, Taber A, Balcioglu M, Vang S, Assaf Z, Sharma S, Tin AS, Srinivasan R, Hafez D, Reinert T, Navarro S, Olson A, Ram R, Dashner S, Rabinowitz M, Billings P, Sigurjonsson S, Andersen CL, Swenerton R, Aleshin A, Zimmermann B, Agerbæk M, Lin CHJ, Jensen JB, Dyrskjøt L. Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma. J Clin Oncol 2019; 37:1547-1557. [PMID: 31059311 DOI: 10.1200/jco.18.02052] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy. PATIENTS AND METHODS We included 68 patients with localized advanced bladder cancer. Patient-specific somatic mutations, identified by whole-exome sequencing, were used to assess circulating tumor DNA (ctDNA) by ultra-deep sequencing (median, 105,000×) of plasma DNA. Plasma samples (n = 656) were procured at diagnosis, during chemotherapy, before cystectomy, and during surveillance. Expression profiling was performed for tumor subtype and immune signature analyses. RESULTS Presence of ctDNA was highly prognostic at diagnosis before chemotherapy (hazard ratio, 29.1; P = .001). After cystectomy, ctDNA analysis correctly identified all patients with metastatic relapse during disease monitoring (100% sensitivity, 98% specificity). A median lead time over radiographic imaging of 96 days was observed. In addition, for high-risk patients (ctDNA positive before or during treatment), the dynamics of ctDNA during chemotherapy was associated with disease recurrence (P = .023), whereas pathologic downstaging was not. Analysis of tumor-centric biomarkers showed that mutational processes (signature 5) were associated with pathologic downstaging (P = .024); however, no significant correlation for tumor subtypes, DNA damage response mutations, and other biomarkers was observed. Our results suggest that ctDNA analysis is better associated with treatment efficacy compared with other available methods. CONCLUSION ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ann Taber
- 1 Aarhus University Hospital, Aarhus, Denmark
| | | | - Søren Vang
- 1 Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lars Dyrskjøt
- 1 Aarhus University Hospital, Aarhus, Denmark.,3 Aarhus University, Aarhus, Denmark
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22
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McCoy R, Demko Z, Ryan A, Banjevic M, Hill M, Sigurjonsson S, Rabinowitz M, Fraser H, Petrov D. Common variants associated with mitotic-origin of aneuploidy in human embryos. Reprod Biomed Online 2018. [DOI: 10.1016/j.rbmo.2017.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Quinn AM, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2018; 554:264. [PMID: 29258292 DOI: 10.1038/nature25161] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This corrects the article DOI: 10.1038/nature22364.
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24
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Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2017; 545:446-451. [PMID: 28445469 PMCID: PMC5812436 DOI: 10.1038/nature22364] [Citation(s) in RCA: 1092] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/13/2017] [Indexed: 12/13/2022]
Abstract
The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.
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MESH Headings
- Biopsy/methods
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/surgery
- Cell Lineage/genetics
- Cell Tracking
- Clone Cells/metabolism
- Clone Cells/pathology
- DNA Mutational Analysis
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Early Detection of Cancer/methods
- Evolution, Molecular
- Humans
- Limit of Detection
- Lung Neoplasms/blood
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/surgery
- Multiplex Polymerase Chain Reaction
- Neoplasm Metastasis/diagnosis
- Neoplasm Metastasis/genetics
- Neoplasm Metastasis/pathology
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Postoperative Care/methods
- Reproducibility of Results
- Tumor Burden
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Affiliation(s)
- Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Tudor Constantin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Raheleh Salari
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - John Le Quesne
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - David A Moore
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Teresa Marafioti
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Eser Kirkizlar
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Thomas B K Watkins
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luke Martinson
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Joan Riley
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Francesco Fraioli
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Maise Al Bakir
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francisco Zambrana
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Raymondo Endozo
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Wenya Linda Bi
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fiona M Fennessy
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Sponer
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Justyna Czyzewska-Khan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tim Chambers
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tumour Profiling Unit Genomics Facility, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Samra Turajlic
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Mary Falzon
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Elaine Borg
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - David Lawrence
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Martin Hayward
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Shyam Kolvekar
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Nikolaos Panagiotopoulos
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Sam M Janes
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, Rayne Building, University College London, 5 University Street, London WC1E 6JF, UK
| | - Ricky Thakrar
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Fiona Blackhall
- Institute of Cancer Studies, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- The Christie Hospital, Manchester M20 4BX, UK
| | | | - Dina Hafez
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Ashwini Naik
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Apratim Ganguly
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Stephanie Kareht
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Rajesh Shah
- Department of Cardiothoracic Surgery, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Leena Joseph
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Anne Marie Quinn
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Phil A Crosbie
- North West Lung Centre, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Babu Naidu
- Department of Thoracic Surgery, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK. University College London Hospitals NHS Foundation Trust, London, UK
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Gerald Langman
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Simon Trotter
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Marianne Nicolson
- Department of Medical Oncology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Hardy Remmen
- Department of Cardiothoracic Surgery, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Keith Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Mahendran Chetty
- Department of Respiratory Medicine, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Lesley Gomersall
- Department of Radiology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Dean A Fennell
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Apostolos Nakas
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Sridhar Rathinam
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Girija Anand
- Department of Radiotherapy, North Middlesex University Hospital, London N18 1QX, UK
| | - Sajid Khan
- Department of Respiratory Medicine, Royal Free Hospital, Pond Street, London NW3 2QG, UK
- Department of Respiratory Medicine, Barnet and Chase Farm Hospitals, Wellhouse Lane, Barnet EN5 3DJ, UK
| | - Peter Russell
- Department of Respiratory Medicine, The Princess Alexandra Hospital, Hamstel Road, Harlow CM20 1QX, UK
| | - Veni Ezhil
- Department of Clinical Oncology, St.Luke's Cancer Centre, Royal Surrey County Hospital, Guildford GU2 7XX, UK
| | - Babikir Ismail
- Department of Pathology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Melanie Irvin-Sellers
- Department of Respiratory Medicine, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Vineet Prakash
- Department of Radiology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Jason F Lester
- Department of Clinical Oncology, Velindre Hospital, Cardiff CF14 2TL, UK
| | | | - Richard Attanoos
- Department of Cellular Pathology, University Hospital of Wales and Cardiff University, Heath Park, Cardiff, UK
| | - Haydn Adams
- Department of Radiology, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Helen Davies
- Department of Respiratory Medicine, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Dahmane Oukrif
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Ayse U Akarca
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - John A Hartley
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Helen L Lowe
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Sara Lock
- Department of Respiratory Medicine, The Whittington Hospital NHS Trust, London, N19 5NF, UK
| | - Natasha Iles
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Harriet Bell
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Yenting Ngai
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Greg Elgar
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Aengus Stewart
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Karl S Peggs
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Research Department of Haematology, University College Cancer Institute, London WC1E 6DD, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Caroline Dive
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - C Jimmy Lin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | | | - Hugo J W L Aerts
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215-5450, USA
| | - Allan Hackshaw
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Jacqui A Shaw
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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McNally L, Huynh D, Keller J, Dikan J, Rabinowitz M, Lathi RB. Patient Experience with Karyotyping After First Trimester Miscarriage: A National Survey. J Reprod Med 2016; 61:128-132. [PMID: 27172634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To assess the frequency of chromosome testing after first trimester miscarriage as well as to investigate patient experiences. STUDY DESIGN An anonymous online questionnaire was developed and made available. Inclusion criteria were female, age ≥ 18, first trimester miscarriage, occurrence of miscarriage within the past year, miscarriage care provided in the United States, and survey completion. RESULTS Of the 980 women who started the survey, 448 met inclusion criteria. Of those, 37 participants had chromosome testing on the miscarriage specimen. Of those who did not have testing, 66% said they wished they had done so at the time of miscarriage, and 67% said they would still want testing if it were available today. There was no correlation between patient age and chromosome testing. Chromosome testing increased in frequency with higher number of miscarriages, although the low number of women with chromosome testing limits our ability to draw definitive conclusions. On average, providers needed to spend 15-20 minutes with patients for them to feel like it was "enough time." CONCLUSION In this national survey we found that chromosome testing is performed in approximately 8% of first trimester miscarriages. Our data indicate that the majority of patients experiencing first trimester miscarriage desire chromosome testing.
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Kirkizlar E, Zimmermann B, Constantin T, Swenerton R, Hoang B, Wayham N, Babiarz JE, Demko Z, Pelham RJ, Kareht S, Simon AL, Jinnett KN, Rabinowitz M, Sigurjonsson S, Hill M. Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology. Transl Oncol 2015; 8:407-416. [PMID: 26500031 PMCID: PMC4631096 DOI: 10.1016/j.tranon.2015.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/31/2015] [Accepted: 08/10/2015] [Indexed: 12/20/2022] Open
Abstract
We demonstrate proof-of-concept for the use of massively multiplexed PCR and next-generation sequencing (mmPCR-NGS) to identify both clonal and subclonal copy-number variants (CNVs) in circulating tumor DNA. This is the first report of a targeted methodology for detection of CNVs in plasma. Using an in vitro model of cell-free DNA, we show that mmPCR-NGS can accurately detect CNVs with average allelic imbalances as low as 0.5%, an improvement over previously reported whole-genome sequencing approaches. Our method revealed differences in the spectrum of CNVs detected in tumor tissue subsections and matching plasma samples from 11 patients with stage II breast cancer. Moreover, we showed that liquid biopsies are able to detect subclonal mutations that may be missed in tumor tissue biopsies. We anticipate that this mmPCR-NGS methodology will have broad applicability for the characterization, diagnosis, and therapeutic monitoring of CNV-enriched cancers, such as breast, ovarian, and lung cancer.
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Affiliation(s)
- Eser Kirkizlar
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | | | - Tudor Constantin
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Ryan Swenerton
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Bin Hoang
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Nicholas Wayham
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Joshua E Babiarz
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Zachary Demko
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Robert J Pelham
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | - Stephanie Kareht
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070
| | | | | | | | | | - Matthew Hill
- Natera Inc., 201 Industrial Road, Suite 410, San Carlos, CA 94070.
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Simon AL, Su B, Demko Z, Rabinowitz M, Harmon ER, Gross SJ. Detection of complete molar pregnancy by single-nucleotide polymorphism-based non-invasive prenatal testing. Ultrasound Obstet Gynecol 2015; 46:506-507. [PMID: 25810270 DOI: 10.1002/uog.14854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/05/2015] [Accepted: 03/17/2015] [Indexed: 06/04/2023]
Affiliation(s)
- A L Simon
- Natera, Inc., 201 Industrial Road, Suite 410, San Carlos, CA, 94070, USA
| | - B Su
- Natera, Inc., 201 Industrial Road, Suite 410, San Carlos, CA, 94070, USA
| | - Z Demko
- Natera, Inc., 201 Industrial Road, Suite 410, San Carlos, CA, 94070, USA
| | - M Rabinowitz
- Natera, Inc., 201 Industrial Road, Suite 410, San Carlos, CA, 94070, USA
| | | | - S J Gross
- Natera, Inc., 201 Industrial Road, Suite 410, San Carlos, CA, 94070, USA
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McCoy RC, Demko ZP, Ryan A, Banjevic M, Hill M, Sigurjonsson S, Rabinowitz M, Petrov DA. Evidence of Selection against Complex Mitotic-Origin Aneuploidy during Preimplantation Development. PLoS Genet 2015; 11:e1005601. [PMID: 26491874 PMCID: PMC4619652 DOI: 10.1371/journal.pgen.1005601] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/21/2015] [Indexed: 11/18/2022] Open
Abstract
Whole-chromosome imbalances affect over half of early human embryos and are the leading cause of pregnancy loss. While these errors frequently arise in oocyte meiosis, many such whole-chromosome abnormalities affecting cleavage-stage embryos are the result of chromosome missegregation occurring during the initial mitotic cell divisions. The first wave of zygotic genome activation at the 4-8 cell stage results in the arrest of a large proportion of embryos, the vast majority of which contain whole-chromosome abnormalities. Thus, the full spectrum of meiotic and mitotic errors can only be detected by sampling after the initial cell divisions, but prior to this selective filter. Here, we apply 24-chromosome preimplantation genetic screening (PGS) to 28,052 single-cell day-3 blastomere biopsies and 18,387 multi-cell day-5 trophectoderm biopsies from 6,366 in vitro fertilization (IVF) cycles. We precisely characterize the rates and patterns of whole-chromosome abnormalities at each developmental stage and distinguish errors of meiotic and mitotic origin without embryo disaggregation, based on informative chromosomal signatures. We show that mitotic errors frequently involve multiple chromosome losses that are not biased toward maternal or paternal homologs. This outcome is characteristic of spindle abnormalities and chaotic cell division detected in previous studies. In contrast to meiotic errors, our data also show that mitotic errors are not significantly associated with maternal age. PGS patients referred due to previous IVF failure had elevated rates of mitotic error, while patients referred due to recurrent pregnancy loss had elevated rates of meiotic error, controlling for maternal age. These results support the conclusion that mitotic error is the predominant mechanism contributing to pregnancy losses occurring prior to blastocyst formation. This high-resolution view of the full spectrum of whole-chromosome abnormalities affecting early embryos provides insight into the cytogenetic mechanisms underlying their formation and the consequences for human fertility.
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Affiliation(s)
- Rajiv C. McCoy
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Allison Ryan
- Natera, Inc., San Carlos, California, United States of America
| | - Milena Banjevic
- Natera, Inc., San Carlos, California, United States of America
| | - Matthew Hill
- Natera, Inc., San Carlos, California, United States of America
| | | | | | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
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Rabinowitz M, McCoy R, Fischer E, Proctor G, Demko Z, Simon A, Ryan A, Kiehl M, Petrov D, Givens C, Bush M. Analyses of 37,000+ embryos with 24-chromosome single-nucleotide polymorphism (SNP)-based preimplantation genetic screening (PGS). Fertil Steril 2015. [DOI: 10.1016/j.fertnstert.2015.07.888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Benn P, Curnow KJ, Chapman S, Michalopoulos SN, Hornberger J, Rabinowitz M. An Economic Analysis of Cell-Free DNA Non-Invasive Prenatal Testing in the US General Pregnancy Population. PLoS One 2015; 10:e0132313. [PMID: 26158465 PMCID: PMC4497716 DOI: 10.1371/journal.pone.0132313] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/11/2015] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Analyze the economic value of replacing conventional fetal aneuploidy screening approaches with non-invasive prenatal testing (NIPT) in the general pregnancy population. METHODS Using decision-analysis modeling, we compared conventional screening to NIPT with cell-free DNA (cfDNA) analysis in the annual US pregnancy population. Sensitivity and specificity for fetal aneuploidies, trisomy 21, trisomy 18, trisomy 13, and monosomy X, were estimated using published data and modeling of both first- and second trimester screening. Costs were assigned for each prenatal test component and for an affected birth. The overall cost to the healthcare system considered screening costs, the number of aneuploid cases detected, invasive procedures performed, procedure-related euploid losses, and affected pregnancies averted. Sensitivity analyses evaluated the effect of variation in parameters. Costs were reported in 2014 US Dollars. RESULTS Replacing conventional screening with NIPT would reduce healthcare costs if it can be provided for $744 or less in the general pregnancy population. The most influential variables were timing of screening entry, screening costs, and pregnancy termination rates. Of the 13,176 affected pregnancies undergoing screening, NIPT detected 96.5% (12,717/13,176) of cases, compared with 85.9% (11,314/13,176) by conventional approaches. NIPT reduced invasive procedures by 60.0%, with NIPT and conventional methods resulting in 24,596 and 61,430 invasive procedures, respectively. The number of procedure-related euploid fetal losses was reduced by 73.5% (194/264) in the general screening population. CONCLUSION Based on our analysis, universal application of NIPT would increase fetal aneuploidy detection rates and can be economically justified. Offering this testing to all pregnant women is associated with substantial prenatal healthcare benefits.
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Affiliation(s)
- Peter Benn
- Division of Human Genetics, Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States of America
| | | | | | | | - John Hornberger
- Cedar Associates, Menlo Park, CA, United States of America
- Stanford University, Stanford, CA, United States of America
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Pelham RJ, Zimmermann BG, Kirkizlar E, Swenerton RK, Hoang B, Sakarya O, Babiarz JE, Wayham N, Constantin T, Sigurjonsson S, Rabinowitz M, Hill M. Abstract P4-02-03: Detection of single nucleotide variations and copy number variations in breast cancer tissue and ctDNA samples using single-nucleotide polymorphism-targeted massively multiplexed PCR. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p4-02-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic instability, the hallmark of cancer, presents with a variety of mutation types, most commonly single nucleotide variations (SNVs) and copy number variations (CNVs), which traditionally have required different methods for identification. It has proven challenging to simultaneously achieve sufficient breadth to detect CNVs and depth to detect SNVs on samples of limited input amount. The objective of this study was to validate a new methodology for detection of SNVs and CNVs in a single assay. We used a massively multiplex PCR/NGS approach combining an SNV panel covering 585 point mutation hotspots in breast cancer (Cosmic) and a CNV panel targeting 28,000 SNPs designed to detect copy number at chromosomes 1, 2, 13, 18, 21, and X, and focal regions 4p16, 5p15, 7q11, 15q, 17p, 22q11, and 22q13. We applied these panels to breast cancer cell lines and fresh frozen (FF) breast tumor samples; the presence of CNVs in circulating cell-free tumor DNA (ctDNA) in the plasma of breast cancer patients was also investigated.
The CNV assay methodology was validated using genomic DNA isolated from 96 human samples with known karyotype; sensitivity to single region deletions or duplications was 100% (71/71) and specificity was 100% for normal regions in the same samples. Single-molecule sensitivity for the detection of CNVs was established by analyzing isolated single cells. Performance of the mutation assay was demonstrated with the analysis of 5 matched tumor and normal cell lines, with 24 out of 27 SNVs known to be present in these cell lines detected. The 3 undetected SNVs were determined to be a result of assay design failure. Also, multiple somatic CNVs (median: 13) were detected in all 5 tumor cell lines. Analysis of the normal cell lines found no cancer related SNVs or CNVs.
In 32 FF tumor samples, 78.1% (25/32) had SNVs detected; of samples with SNVs, 88% (22/25) had SNVs in TP53 or PIK3CA. Of the same 32 FF breast tumor samples, 96.9% (31/32) showed full or partial CNVs in at least 1 and up to 15 regions; of the 31 samples with detected CNVs, 93.5% had a CNV of either 1q or 17p, two of the three most prevalent breast cancer CNVs (the 16q region was not represented in this panel). Overall, a combination of SNV and CNV testing allowed identification of genetic changes in 100% of the breast tumor samples, a significant improvement in diagnostic yield than using SNV detection alone.
Of the 12 breast cancer patients with matched tumor tissue and plasma samples, 83.3% (10/12) had CNVs detected in tissue. The CNVs present in each primary tumor sample were identified in corresponding plasma ctDNA samples (1 stage IIa, 7 stage IIb, and 2 stage III). The ctDNA fractions in these samples ranged from 0.58 to 4.33%; detection required as few as 86 heterozygous SNPs per CNV.
Analysis of ctDNA for cancer-associated mutations may allow earlier, safer and more accurate profiling and monitoring of breast cancer. Thus, this targeted PCR approach offers the promise of an assay able to detect both cancer-associated SNVs and CNVs in the same sample with good sensitivity and specificity, and improved detection rates compared to assays that only detect SNVs.
Citation Format: Robert J Pelham, Bernhard G Zimmermann, Eser Kirkizlar, Ryan K Swenerton, Bin Hoang, Onur Sakarya, Joshua E Babiarz, Nicholas Wayham, Tudor Constantin, Styrmir Sigurjonsson, Matthew Rabinowitz, Matthew Hill. Detection of single nucleotide variations and copy number variations in breast cancer tissue and ctDNA samples using single-nucleotide polymorphism-targeted massively multiplexed PCR [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-03.
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McCoy RC, Demko Z, Ryan A, Banjevic M, Hill M, Sigurjonsson S, Rabinowitz M, Fraser HB, Petrov DA. Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. Science 2015; 348:235-8. [PMID: 25859044 DOI: 10.1126/science.aaa3337] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aneuploidy, the inheritance of an atypical chromosome complement, is common in early human development and is the primary cause of pregnancy loss. By screening day-3 embryos during in vitro fertilization cycles, we identified an association between aneuploidy of putative mitotic origin and linked genetic variants on chromosome 4 of maternal genomes. This associated region contains a candidate gene, Polo-like kinase 4 (PLK4), that plays a well-characterized role in centriole duplication and has the ability to alter mitotic fidelity upon minor dysregulation. Mothers with the high-risk genotypes contributed fewer embryos for testing at day 5, suggesting that their embryos are less likely to survive to blastocyst formation. The associated region coincides with a signature of a selective sweep in ancient humans, suggesting that the causal variant was either the target of selection or hitchhiked to substantial frequency.
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Affiliation(s)
- Rajiv C McCoy
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | | | | | | | | | | | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
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Kumar A, Ryan A, Kitzman JO, Wemmer N, Snyder MW, Sigurjonsson S, Lee C, Banjevic M, Zarutskie PW, Lewis AP, Shendure J, Rabinowitz M. Whole genome prediction for preimplantation genetic diagnosis. Genome Med 2015; 7:35. [PMID: 26019723 PMCID: PMC4445980 DOI: 10.1186/s13073-015-0160-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/24/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (<36 h) required for fresh embryo transfer. Here, we describe and validate a method for inferring the inherited whole genome sequence of an embryo for preimplantation genetic diagnosis (PGD). METHODS We combine haplotype-resolved, parental genome sequencing with rapid embryo genotyping to predict the whole genome sequence of a day-5 human embryo in a couple at risk of transmitting alpha-thalassemia. RESULTS Inheritance was predicted at approximately 3 million paternally and/or maternally heterozygous sites with greater than 99% accuracy. Furthermore, we successfully phase and predict the transmission of an HBA1/HBA2 deletion from each parent. CONCLUSIONS Our results suggest that preimplantation whole genome prediction may facilitate the comprehensive diagnosis of diseases with a known genetic basis in embryos.
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Affiliation(s)
- Akash Kumar
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Jacob O Kitzman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Matthew W Snyder
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Choli Lee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Paul W Zarutskie
- Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
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Wapner RJ, Babiarz JE, Levy B, Stosic M, Zimmermann B, Sigurjonsson S, Wayham N, Ryan A, Banjevic M, Lacroute P, Hu J, Hall MP, Demko Z, Siddiqui A, Rabinowitz M, Gross SJ, Hill M, Benn P. Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes. Am J Obstet Gynecol 2015; 212:332.e1-9. [PMID: 25479548 DOI: 10.1016/j.ajog.2014.11.041] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/05/2014] [Accepted: 11/30/2014] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The purpose of this study was to estimate the performance of a single-nucleotide polymorphism (SNP)-based noninvasive prenatal test for 5 microdeletion syndromes. STUDY DESIGN Four hundred sixty-nine samples (358 plasma samples from pregnant women, 111 artificial plasma mixtures) were amplified with the use of a massively multiplexed polymerase chain reaction, sequenced, and analyzed with the use of the Next-generation Aneuploidy Test Using SNPs algorithm for the presence or absence of deletions of 22q11.2, 1p36, distal 5p, and the Prader-Willi/Angelman region. RESULTS Detection rates were 97.8% for a 22q11.2 deletion (45/46) and 100% for Prader-Willi (15/15), Angelman (21/21), 1p36 deletion (1/1), and cri-du-chat syndromes (24/24). False-positive rates were 0.76% for 22q11.2 deletion syndrome (3/397) and 0.24% for cri-du-chat syndrome (1/419). No false positives occurred for Prader-Willi (0/428), Angelman (0/442), or 1p36 deletion syndromes (0/422). CONCLUSION SNP-based noninvasive prenatal microdeletion screening is highly accurate. Because clinically relevant microdeletions and duplications occur in >1% of pregnancies, regardless of maternal age, noninvasive screening for the general pregnant population should be considered.
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Ryan A, Demko Z, Sigurjonsson S, Rabinowitz M. Response to Drábek and Cereda. Genet Med 2014; 16:794. [PMID: 25290260 DOI: 10.1038/gim.2014.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 06/26/2014] [Indexed: 11/09/2022] Open
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Pergament E, Cuckle H, Zimmermann B, Banjevic M, Sigurjonsson S, Ryan A, Hall MP, Dodd M, Lacroute P, Stosic M, Chopra N, Hunkapiller N, Prosen DE, McAdoo S, Demko Z, Siddiqui A, Hill M, Rabinowitz M. Single-nucleotide polymorphism-based noninvasive prenatal screening in a high-risk and low-risk cohort. Obstet Gynecol 2014; 124:210-218. [PMID: 25004354 PMCID: PMC4144440 DOI: 10.1097/aog.0000000000000363] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To estimate performance of a single-nucleotide polymorphism-based noninvasive prenatal screen for fetal aneuploidy in high-risk and low-risk populations on single venopuncture. METHODS One thousand sixty-four maternal blood samples from 7 weeks of gestation and beyond were included; 1,051 were within specifications and 518 (49.3%) were low risk. Cell-free DNA was amplified, sequenced, and analyzed using the Next-generation Aneuploidy Test Using SNPs algorithm. Samples were called as trisomies 21, 18, 13, or monosomy X, or euploid, and male or female. RESULTS Nine hundred sixty-six samples (91.9%) successfully generated a cell-free DNA result. Among these, sensitivity was 100% for trisomy 21 (58/58, confidence interval [CI] 93.8-100%), trisomy 13 (12/12, CI 73.5-100%), and fetal sex (358/358 female, CI 99.0-100%; 418/418 male, CI 99.1-100%), 96.0% for trisomy 18 (24/25, CI 79.7-99.9%), and 90% for monosomy X (9/10, CI 55.5-99.8%). Specificity for trisomies 21 and 13 was 100% (905/905, CI 99.6-100%; and 953/953, CI 99.6-100%, respectively) and for trisomy 18 and monosomy X was 99.9% (938/939, CI 99.4-100%; and 953/954, CI 99.4-100%, respectively). However, 16% (20/125) of aneuploid samples did not return a result; 50% (10/20) had a fetal fraction below the 1.5th percentile of euploid pregnancies. Aneuploidy rate was significantly higher in these samples (P<.001, odds ratio 9.2, CI 4.4-19.0). Sensitivity and specificity did not differ in low-risk and high-risk populations. CONCLUSIONS This noninvasive prenatal screen performed with high sensitivity and specificity in high-risk and low-risk cohorts. Aneuploid samples were significantly more likely to not return a result; the number of aneuploidy samples was especially increased among samples with low fetal fraction. This underscores the importance of redraws or, in rare cases, invasive procedures based on low fetal fraction. LEVEL OF EVIDENCE II.
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Zimmermann BG, Kirkizlar E, Hill M, Constantin T, Sigurjonsson S, Hoanga B, Chopra N, Rabinowitz M. Non-invasive Cell-free Tumor DNA-based Detection of Breast Cancer-related Copy Number Variations. Cancer Genet 2014. [DOI: 10.1016/j.cancergen.2014.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Babiarz JE, Zimmermann BG, Constantin T, Swenerton R, Kirkizlar E, Wayham N, Rabinowitz M, Hill M. Detection of Copy Number Variations in Breast Cancer Samples Using Single-nucleotide Polymorphism-targeted Massively Multiplexed PCR. Cancer Genet 2014. [DOI: 10.1016/j.cancergen.2014.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hall MP, Hill M, Zimmermann B, Sigurjonsson S, Westemeyer M, Saucier J, Demko Z, Rabinowitz M. Non-invasive prenatal detection of trisomy 13 using a single nucleotide polymorphism- and informatics-based approach. PLoS One 2014; 9:e96677. [PMID: 24805989 PMCID: PMC4013011 DOI: 10.1371/journal.pone.0096677] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/11/2014] [Indexed: 01/08/2023] Open
Abstract
Purpose To determine how a single nucleotide polymorphism (SNP)- and informatics-based non-invasive prenatal aneuploidy test performs in detecting trisomy 13. Methods Seventeen trisomy 13 and 51 age-matched euploid samples, randomly selected from a larger cohort, were analyzed. Cell-free DNA was isolated from maternal plasma, amplified in a single multiplex polymerase chain reaction assay that interrogated 19,488 SNPs covering chromosomes 13, 18, 21, X, and Y, and sequenced. Analysis and copy number identification involved a Bayesian-based maximum likelihood statistical method that generated chromosome- and sample-specific calculated accuracies. Results Of the samples that passed a stringent DNA quality threshold (94.1%), the algorithm correctly identified 15/15 trisomy 13 and 49/49 euploid samples, for 320/320 correct copy number calls. Conclusions This informatics- and SNP-based method accurately detects trisomy 13-affected fetuses non-invasively and with high calculated accuracy.
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Affiliation(s)
- Megan P. Hall
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Matthew Hill
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Bernhard Zimmermann
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Styrmir Sigurjonsson
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
| | - Margaret Westemeyer
- Department of Genetic Counseling, Natera Inc., San Carlos, California, United States of America
| | - Jennifer Saucier
- Department of Genetic Counseling, Natera Inc., San Carlos, California, United States of America
| | - Zachary Demko
- Department of Genetic Counseling, Natera Inc., San Carlos, California, United States of America
| | - Matthew Rabinowitz
- Department of Research and Development, Natera Inc., San Carlos, California, United States of America
- * E-mail:
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Rabinowitz M. Comment on "Commercial landscape of noninvasive prenatal testing in the United States". Prenat Diagn 2013; 33:913. [PMID: 23996704 PMCID: PMC3793235 DOI: 10.1002/pd.4185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/23/2013] [Indexed: 11/08/2022]
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Maisenbacher M, Clark D, Cheung E, Pettersen B, Lathi R, Rabinowitz M. Informatics-based molecular karyotyping of products of conception (POC): focus on molar pregnancies. Fertil Steril 2013. [DOI: 10.1016/j.fertnstert.2013.07.1013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hall M, Hill M, Zimmerman B, Sigurjonsson S, Demko Z, Rabinowitz M. Triploidy detection via single nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT): two case studies. Fertil Steril 2013. [DOI: 10.1016/j.fertnstert.2013.07.1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Samango-Sprouse C, Banjevic M, Ryan A, Sigurjonsson S, Zimmermann B, Hill M, Hall MP, Westemeyer M, Saucier J, Demko Z, Rabinowitz M. SNP-based non-invasive prenatal testing detects sex chromosome aneuploidies with high accuracy. Prenat Diagn 2013; 33:643-9. [PMID: 23712453 DOI: 10.1002/pd.4159] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 05/06/2013] [Accepted: 05/15/2013] [Indexed: 12/17/2022]
Abstract
OBJECTIVE This study aimed to develop a single-nucleotide polymorphism-based and informatics-based non-invasive prenatal test that detects sex chromosome aneuploidies early in pregnancy. METHODS Sixteen aneuploid samples, including thirteen 45,X, two 47,XXY, and one 47,XYY, along with 185 euploid controls, were analyzed. Cell-free DNA was isolated from maternal plasma, amplified in a single multiplex polymerase chain reaction assay that targeted 19,488 polymorphic loci covering chromosomes 13, 18, 21, X, and Y, and sequenced. Sequencing results were analyzed using a Bayesian-based maximum likelihood statistical method to determine copy number of interrogated chromosomes, calculating sample-specific accuracies. RESULTS Of the samples that passed a stringent quality control metric (93%), the algorithm correctly identified copy number at all five chromosomes in all but one of the 187 samples, for 934/935 correct calls as early as 9.4 weeks of gestation. We detected 45,X with 91.7% sensitivity (CI: 61.5-99.8%) and 100% specificity (CI: 97.9-100%), and 47,XXY and 47,XYY. The average calculated accuracy was 99.78%. CONCLUSION This method non-invasively detected 45,X, 47,XXY, and 47,XYY fetuses from cell-free DNA isolated from maternal plasma with high calculated accuracies and thus offers a non-invasive method with the potential to function as a routine screen allowing for early prenatal detection of rarely diagnosed yet commonly occurring sex aneuploidies.
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Affiliation(s)
- Carole Samango-Sprouse
- George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.
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Lynch C, Tee N, Rouse H, Gordon A, Sati L, Zeiss C, Soygur B, Bassorgun I, Goksu E, Demir R, McGrath J, Groendahl ML, Thuesen L, Andersen AN, Loft A, Smitz J, Adriaenssens T, Vikesa J, Borup R, Mersy E, Kisters N, Macville MVE, Engelen JJM, Consortium SENN, Menheere PPCA, Geraedts JP, Coumans ABC, Frints SGM, Aledani T, Assou S, Traver S, Ait-ahmed O, Dechaud H, Hamamah S, Mizutani E, Suzumori N, Sugiyama C, Hattori Y, Sato T, Ando H, Ozaki Y, Sugiura-Ogasawara M, Wissing M, Kristensen SG, Andersen CY, Mikkelsen AL, Hoest T, Borup R, Groendahl ML, Velthut-Meikas A, Simm J, Metsis M, Salumets A, Palini S, Galluzzi L, De Stefani S, Primiterra M, Wells D, Magnani M, Bulletti C, Vogt PH, Frank-Herrmann P, Bender U, Strowitzki T, Besikoglu B, Heidemann P, Wunsch L, Bettendorf M, Jelinkova L, Vilimova S, Kosarova M, Sebek P, Volemanova E, Kruzelova M, Civisova J, Svobodova L, Sobotka V, Mardesic T, van de Werken C, Santos MA, Eleveld C, Laven JSE, Baart EB, Pylyp LY, Spinenko LA, Zukin VD, Perez-Sanz J, Matorras R, Arluzea J, Bilbao J, Gonzalez-Santiago N, Yeh N, Koff A, Barlas A, Romin Y, Manova-Todorova K, Hoz CDL, Mauri AL, Nascimento AM, Vagnini LD, Petersen CG, Ricci J, Massaro FC, Cavagna M, Pontes A, Oliveira JBA, Baruffi RLR, Franco JG, Wu EX, Ma S, Parriego M, Sole M, Boada M, Coroleu B, Veiga A, Kakourou G, Poulou M, Vrettou C, Destouni A, Traeger-Synodinos J, Kanavakis E, Yatsenko AN, Georgiadis AP, McGuire MM, Zorrilla M, Bunce KD, Peters D, Rajkovic A, Olszewska M, Kurpisz M, Gilbertson AZA, Ottolini CS, Summers MC, Sage K, Handyside AH, Thornhill AR, Griffin DK, Chung MK, Kim JW, Lee JH, Jeong HJ, Kim MH, Ryu MJ, Park SJ, Kang HY, Lee HS, Zimmermann B, Banjevic M, Hill M, Lacroute P, Dodd M, Sigurjonsson S, Lau P, Prosen D, Chopra N, Ryan A, Hall M, McAdoo S, Demko Z, Levy B, Rabinowitz M, Vereczeky A, Kosa ZS, Savay S, Csenki M, Nanassy L, Dudas B, Domotor ZS, Debreceni D, Rossi A, Alegretti JR, Cuzzi J, Bonavita M, Tanada M, Matunaga P, Fettback P, Rosa MB, Maia V, Hassun P, Motta ELA, Piccolomini M, Gomes C, Barros B, Nicoliello M, Matunaga P, Criscuolo T, Bonavita M, Alegretti JR, Miyadahira E, Cuzzi J, Hassun P, Motta ELA, Montjean D, Benkhalifa M, Berthaut I, Griveau JF, Morcel K, Bashamboo A, McElreavey K, Ravel C, Rubio C, Rodrigo L, Mateu E, Mercader A, Peinado V, Buendia P, Milan M, Delgado A, Al-Asmar N, Escrich L, Campos-Galindo I, Garcia-Herrero S, Poo ME, Mir P, Simon C, Reyes-Engel A, Cortes-Rodriguez M, Lendinez A, Perez-Nevot B, Palomares AR, Galdon MR, Ruberti A, Minasi MG, Biricik A, Colasante A, Zavaglia D, Iammarrone E, Fiorentino F, Greco E, Demir N, Ozturk S, Sozen B, Morales R, Lledo B, Ortiz JA, Ten J, Llacer J, Bernabeu R, Nagayoshi M, Tanaka A, Tanaka I, Kusunoki H, Watanabe S, Temel SG, Beyazyurek C, Ekmekci GC, Aybar F, Cinar C, Kahraman S, Nordqvist S, Karehed K, Akerud H, Ottolini CS, Griffin DK, Thornhill AR, Handyside AH, Gultomruk M, Tulay P, Findikli N, Yagmur E, Karlikaya G, Ulug U, Bahceci M, Bargallo MF, Arevalo MR, Salat MM, Barbat IV, Lopez JT, Algam ME, Boluda AB, de Oya GC, Tolmacheva EN, Kashevarova AA, Skryabin NA, Lebedev IN, Semaco E, Belo A, Riboldi M, Cuzzi J, Barros B, Luz L, Criscuolo T, Nobrega N, Matunaga P, Mazetto R, Alegretti JA, Bibancos M, Hassun P, Motta ELA, Serafini P, Neupane J, Vandewoestyne M, Heindryckx B, Deroo T, Lu Y, Ghimire S, Lierman S, Qian C, Deforce D, De Sutter P, Rodrigo L, Rubio C, Mateu E, Peinado V, Milan M, Viloria T, Al-Asmar N, Mercader A, Buendia P, Delgado A, Escrich L, Martinez-Jabaloyas JM, Simon C, Gil-Salom M, Capalbo A, Treff N, Cimadomo D, Tao X, Ferry K, Ubaldi FM, Rienzi L, Scott RT, Katzorke N, Strowitzki T, Vogt HP, Hehr A, Gassner C, Paulmann B, Kowalzyk Z, Klatt M, Krauss S, Seifert D, Seifert B, Hehr U, Minasi MG, Ruberti A, Biricik A, Lobascio M, Zavaglia D, Varricchio MT, Fiorentino F, Greco E, Rubino P, Bono S, Cotarelo RP, Spizzichino L, Biricik A, Colicchia A, Giannini P, Fiorentino F, Suhorutshenko M, Rosenstein-Tamm K, Simm J, Salumets A, Metsis M. Reproductive (epi)genetics. Hum Reprod 2013. [DOI: 10.1093/humrep/det220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Aizpurua J, Szlarb N, Moragues I, Ramos B, Rogel S, Li J, Yin XY, Tan K, Tan YQ, Chen F, Zhang LEI, Lin G, Jiang H, Wang W, Wells D, Kaur K, Grifo J, Anderson S, Taylor J, Fragouli E, Munne S, Levy B, Banjevic M, Hill M, Zimmermann B, Ryan A, Sigurjonsson S, Wayham N, Lacroute P, Dodd M, Hoang B, Tong J, Vu P, Hall MP, Demko Z, Rabinowitz M, Spath K, Fragouli E, Konstantinidis M, Poli M, Wells D. Session 16: Innovations in reproductive genetics. Hum Reprod 2013. [DOI: 10.1093/humrep/det143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Potter D, Merrion K, Pettersen B, Kijacic D, Demko Z, Rabinowitz M. IVF Outcomes on Over 1,200 Day 3 and Day 5 Preimplantation Genetic Screening (PGS) Cycles with 24-chromosome Aneuploidy Testing Using Single Nucleotide Polymorphism (SNP) Microarrays. Fertil Steril 2013. [DOI: 10.1016/j.fertnstert.2013.01.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Potter D, Wemmer N, Merrion K, Hill M, Rabinowitz M. IVF Outcomes on Patients Who Underwent Preimplantation Genetic Diagnosis (PGD) for Inherited Genetic Disorders with Concurrent 24 Chromosome Aneuploidy Screening Using Single Nucleotide Polymorphism (SNP) Microarrays. Fertil Steril 2013. [DOI: 10.1016/j.fertnstert.2013.01.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rabinowitz M, Hill M, Demko Z, McAdoo S, Zimmermann B, Levy B. 591: Using targeted sequencing of SNPs to achieve a highly accurate non-invasive detection of fetal aneuploidy of 13, 18, 21 and sex chromosomes. Am J Obstet Gynecol 2013. [DOI: 10.1016/j.ajog.2012.10.757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ryan A, Baner J, Demko Z, Hill M, Sigurjonsson S, Baird ML, Rabinowitz M. Informatics-based, highly accurate, noninvasive prenatal paternity testing. Genet Med 2012; 15:473-7. [PMID: 23258349 PMCID: PMC3910294 DOI: 10.1038/gim.2012.155] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Purpose: The aim of the study was to evaluate the diagnostic accuracy of an informatics-based, noninvasive, prenatal paternity test using array-based single-nucleotide polymorphism measurements of cell-free DNA isolated from maternal plasma. Methods: Blood samples were taken from 21 adult pregnant women (with gestational ages between 6 and 21 weeks), and a genetic sample was taken from the corresponding biological fathers. Paternity was confirmed by genetic testing of the infant, products of conception, control of fertilization, and/or preimplantation genetic diagnosis during in vitro fertilization. Parental DNA samples and maternal plasma cell-free DNA were amplified and analyzed using a HumanCytoSNP-12 array. An informatics-based method measured single-nucleotide polymorphism data, confirming or rejecting paternity. Each plasma sample with a sufficient fetal cell-free DNA fraction was independently tested against the confirmed father and 1,820 random, unrelated males. Results: One of the 21 samples had insufficient fetal cell-free DNA. The test correctly confirmed paternity for the remaining 20 samples (100%) when tested against the biological father, with P values of <10−4. For the 36,400 tests using an unrelated male as the alleged father, 99.95% (36,382) correctly excluded paternity and 0.05% (18) were indeterminate. There were no miscalls. Conclusion: A noninvasive paternity test using informatics-based analysis of single-nucleotide polymorphism array measurements accurately determined paternity early in pregnancy.
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Zimmermann B, Hill M, Gemelos G, Demko Z, Banjevic M, Baner J, Ryan A, Sigurjonsson S, Chopra N, Dodd M, Levy B, Rabinowitz M. Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci. Prenat Diagn 2012; 32:1233-41. [PMID: 23108718 PMCID: PMC3548605 DOI: 10.1002/pd.3993] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE This study aims to develop a noninvasive prenatal test on the basis of the analysis of cell-free DNA in maternal blood to detect fetal aneuploidy at chromosomes 13, 18, 21, X, and Y. METHODS A total of 166 samples from pregnant women, including 11 trisomy 21, three trisomy 18, two trisomy 13, two 45,X, and two 47,XXY samples, were analyzed using an informatics-based method. Cell-free DNA from maternal blood was isolated, amplified using a multiplex polymerase chain reaction (PCR) assay targeting 11,000 single nucleotide polymorphisms on chromosomes 13, 18, 21, X, and Y in a single reaction, and sequenced. A Bayesian-based maximum likelihood statistical method was applied to determine the chromosomal count of the five chromosomes interrogated in each sample, along with a sample-specific calculated accuracy for each test result. RESULTS The algorithm correctly reported the chromosome copy number at all five chromosomes in 145 samples that passed a DNA quality test, for a total of 725/725 correct calls. The average calculated accuracy for these samples was 99.92%. Twenty-one samples did not pass the DNA quality test. CONCLUSIONS This informatics-based method noninvasively detected fetuses with trisomy 13, 18, and 21, 45,X, and 47,XXY with high sample-specific calculated accuracies for each individual chromosome and across all five chromosomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia, New York
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