Novel Pooling Strategies for Genetic Testing, with Application to Newborn Screening
References
- (2020) Assessment of specimen pooling to conserve SARS CoV-2 testing resources. Amer. J. Clin. Pathol. 153(6):715–718. 10.1093/ajcp/aqaa064Crossref, Google Scholar
- (2005) Complications associated with symptomatic diagnosis in infants with cystic fibrosis. J. Pediatr. (Suppl 3):S37–S41.Crossref, Google Scholar
- Advisory Committee on Heritable Disorders in Newborns and Children (ACHDNC) (2018) Recommended uniform screening panel core conditions. Accessed June 2020. https://www.hrsa.gov/sites/default/files/hrsa/advisory-committees/heritable-disorders/rusp/rusp-uniform-screening-panel.pdf.Google Scholar
- American Red Cross (2021) What happens to donated blood. Accessed June 2021. https://www.redcrossblood.org/donate-blood/blood-donation-process/what-happens-to-donated-blood.html.Google Scholar
- (2018) Adaptive risk-based pooling in public health screening. IISE Trans. 50(9):753–766.Crossref, Google Scholar
- (2019) Optimal risk-based group testing. Management Sci. 65(9):4365–4384.Link, Google Scholar
- (2020) Optimal group testing: Structural properties and robust solutions, with application to public health screening. INFORMS J. Comput. 32(4):895–911.Abstract, Google Scholar
- Baby’s First Test (2019) Accessed June 2020. http://www.babysfirsttest.org/newborn-screening/states.Google Scholar
- (2016) Improving newborn screening for cystic fibrosis using next-generation sequencing technology: A technical feasibility study. Genet. Med. 18(3):231–238.Crossref, Google Scholar
- (2008) Digraphs: Theory, Algorithms and Applications (Springer Science & Business Media, Springer, London).Google Scholar
- (1958) On a routing problem. Quart. Appl. Math. 16(1):87–90.Crossref, Google Scholar
- (2009) Cystic fibrosis foundation practice guidelines for the management of infants with cystic fibrosis transmembrane conductance regulator-related metabolic syndrome during the first two years of life and beyond. J. Pediatr. 155(6):S106–S116.Crossref, Google Scholar
- (2013) A new era in the treatment of cystic fibrosis: Correction of the underlying CFTR defect. Lancet Respir. Med. 1(2):158–163.Crossref, Google Scholar
- (2004) Allocating Resources to Control Infectious Diseases (Springer US, Boston, MA), 443–464.Google Scholar
- California Department of Public Health (CDPH) (2019) Genetic disease screening program. Accessed June 2020. https://www.cdph.ca.gov/Programs/CFH/DGDS/CDPH%20Document%20Library/FY%202019-20%20GDSP%20November%20Estimate%20%201.9.19%20DOF%20Final.pdf.Google Scholar
- (2005) Newborn screening for cystic fibrosis: An opportunity to improve care and outcomes. J. Pediatr. (Suppl 3):S2–S5.Crossref, Google Scholar
- CFTR2 (2020) Accessed April 2020. https://www.cftr2.org/.Google Scholar
- (1982) A partitioning problem with additive objective with an application to optimal inventory groupings for joint replenishment. Oper. Res. 30(5):1018–1022.Link, Google Scholar
- (2009) Introduction to Algorithms (MIT Press, Cambridge, MA).Google Scholar
- (2013) An Introduction to Cystic Fibrosis for Patients and Their Families, 6th ed. (Cystic Fibrosis Foundation).Google Scholar
- (2017) Genomic sequencing in cystic fibrosis newborn screening: what works best, two-tier predefined CFTR mutation panels or second-tier CFTR panel followed by third-tier sequencing? Genet. Med. 19(10):1159–1163.Crossref, Google Scholar
- (2013) Chapter 58 - Cystic Fibrosis. Rimoin D, Pyeritz R, Korf B, eds. Emery and Rimoin’s Principles and Practice of Medical Genetics (Academic Press, Oxford, UK), 1–54.Crossref, Google Scholar
- Cystic Fibrosis Foundation (2009) All fifty states to screen newborns for cystic fibrosis by 2010. Accessed June 2020. https://www.cff.org/About-Us/Media-Center/Press-Releases/All-Fifty-States-to-Screen-Newborns-for-Cystic-Fibrosis-by-2010/.Google Scholar
- Cystic Fibrosis Foundation (2017) Sweat test. Accessed June 2021. https://www.cff.org/What-is-CF/Testing/Sweat-Test/.Google Scholar
- Cystic Fibrosis Foundation (2019) Carrier testing for cystic fibrosis. Accessed in June 2020. https://www.cff.org/What-is-CF/Testing/Carrier-Testing-for-Cystic-Fibrosis/.Google Scholar
- (2020) CFTR variant testing: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet. Med. 22(8):1288–1295.Crossref, Google Scholar
- (1959) A note on two problems in connexion with graphs. Numer. Math. 1(1):269–271.Crossref, Google Scholar
- (2002) Current prevalence and incidence of infectious disease markers and estimated window-period risk in the American Red Cross blood donor population. Transfusion 42(8):975–979.Crossref, Google Scholar
- (1943) The detection of defective members of large populations. Ann. Math. Statist. 14(4):436–440.Crossref, Google Scholar
- (2015) Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR. J. Clin. Microbiol. 53(3):1002–1004.Crossref, Google Scholar
- (2014) Cystic fibrosis: An inherited disease affecting mucin-producing organs. Internat. J. Biochem. Cell Biol. 52:136–145.Crossref, Google Scholar
- (2018) Robust post-donation blood screening under prevalence rate uncertainty. Oper. Res. 66(1):1–17.Link, Google Scholar
- (2021a) Optimal genetic screening for cystic fibrosis. Oper. Res. 70(1):265–287.Google Scholar
- (2021b) Equity in genetic newborn screening. Naval Res. Logist. 68(1):44–64.Crossref, Google Scholar
- (2022) Screening multi-dimensional heterogeneous populations for infectious diseases under scarce testing resources, with application to covid-19. Naval Res. Logist. 69(1):3–20.Crossref, Google Scholar
- (2005) Sweat-testing in preterm and full-term infants less than 6 weeks of age. Pediatr. Pulmonol. 40(1):64–67.Crossref, Google Scholar
- (2005) Evidence on improved outcomes with early diagnosis of cystic fibrosis through neonatal screening: Enough is enough! Pediatrics 147(Suppl 3):S30–S36.Crossref, Google Scholar
- Food and Drug Administration (2005) CFTR gene mutation detection systems - Class II special controls guidance for industry and FDA staff. Accessed June 2021. https://www.fda.gov/medical-devices/guidance-documents-medical-devices-and-radiation-emitting-products/cftr-gene-mutation-detection-systems-class-ii-special-controls-guidance-industry-and-fda-staff.Google Scholar
- (1956) Network flow theory. Technical report, Rand Corp, Santa Monica CA.Google Scholar
- ; CARE Consortium Investigators, (2020) Data-driven stochastic optimization approaches to determine decision thresholds for risk estimation models. IISE Trans. 52(10):1098–1121.Crossref, Google Scholar
- Gilányi A, ed. (2009) Subadditive Functions (Birkhäuser Basel), 455–481.Google Scholar
- (2015) Showing value in newborn screening: Challenges in quantifying the effectiveness and cost-effectiveness of early detection of phenylketonuria and cystic fibrosis. Health Care (Don Mills). 3(4):1133–1157.Google Scholar
- (2004) Newborn screening for cystic fibrosis: Evaluation of benefits and risks and recommendations for state newborn screening programs. MMWR Recomm Rep. 53(40):1–36.Google Scholar
- (2003) Offering preconceptional cystic fibrosis carrier couple screening in the absence of established preconceptional care services. Public Health Genomics 6(1):5–13.Crossref, Google Scholar
- (2018) Prediction of findings at screening colonoscopy using a machine learning algorithm based on complete blood counts (colonflag). PLoS One 13:1–9, 11. 10.1371/journal.pone.0207848Crossref, Google Scholar
- (2015) Clinical sensitivity of cystic fibrosis mutation panels in a diverse population. Hum. Mutat. 37(2):201–208.Crossref, Google Scholar
- (1975) A generalized binomial group testing problem. J. Amer. Statist. Assoc. 70(352):923–926.Crossref, Google Scholar
- Johns Hopkins Medicine (2019) Cystic fibrosis and CF-related disorders NGS panel. Accessed June 2020. https://www.hopkinsmedicine.org/dnadiagnostic/tests/tests/cystic-fibrosis-and-cf-related-disorders-ngs-panel.Google Scholar
- (2007) A comparative study of five technologically diverse CFTR testing platforms. J. Mol. Diagn. 9(3):401–407.Crossref, Google Scholar
- (2006) Comprehensive genetic analysis of the cystic fibrosis transmembrane conductance regulator from dried blood specimens–implications for newborn screening. Genet. Med. 8(9):557–562.Crossref, Google Scholar
- (2015) Screening for cystic fibrosis in New York state: Considerations for algorithm improvements. Eur. J. Pediatr. 175(2):181–193.Crossref, Google Scholar
- (1989) Identification of the cystic fibrosis gene: Genetic analysis. Science 245(4922):1073–1080.Crossref, Google Scholar
- (2015) Newborn screening for cystic fibrosis in California. Pediatrics 136(6):1062–1072.Crossref, Google Scholar
- (2007) Comparison of group testing algorithms for case identification in the presence of test error. Biometrics 63(4):1152–1163.Crossref, Google Scholar
- (2020) Pooling upper respiratory specimens for rapid mass screening of COVID-19 by real-time RT-PCR. Emerg. Infect. Dis. 26(10):2469.Crossref, Google Scholar
- (2009) Clarification of laboratory and clinical variables that influence cystic fibrosis newborn screening with initial analysis of immunoreactive trypsinogen. Pediatrics 123(2):e338–e346.Crossref, Google Scholar
- (2017) Validation of a novel copy number variant detection algorithm for CFTR from targeted next generation sequencing data. Fertil. Steril. 108(3):e269.Crossref, Google Scholar
- (1992) Rapid and simultaneous detection of multiple mutations by pooled and multiplex single nucleotide primer extension: Application to the study of insulin-responsive glucose transporter and insulin receptor mutations in non-insulin-dependent diabetes. Hum. Mol. Genet. 1(6):391–395.Crossref, Google Scholar
- (2013) Colorectal cancer screening-optimizing current strategies and new directions. Nat. Rev. Clin. Oncol. 10(3):130.Crossref, Google Scholar
- (2002) Newborn screening for cystic fibrosis. Lab. Med. 33(3):212–213.Crossref, Google Scholar
- (2012) Cost savings and increased efficiency using a stratified specimen pooling strategy for Chlamydia Trachomatis and Neisseria Gonorrhoeae. Sex. Transm. Dis. 39(1):46–48.Crossref, Google Scholar
- (2016) Targeted mutation screening panels expose systematic population bias in detection of cystic fibrosis risk. Genet. Med. 18(2):174.Crossref, Google Scholar
- (2008) Cancer screening: A mathematical model relating secreted blood biomarker levels to tumor sizes. PLOS Med. 5:1–11.Crossref, Google Scholar
- (2014) Sweat conductivity: An accurate diagnostic test for cystic fibrosis? J. Cyst. Fibros. 13(5):528–533.Crossref, Google Scholar
- (2012) Informative Dorfman screening. Biometrics 68(1):287–296.Crossref, Google Scholar
- (2007) A global perspective on newborn screening for cystic fibrosis. Curr. Opin. Pulm. Med. 13(6):510–514.Crossref, Google Scholar
- (2019) A methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution. J. Transl. Med. 17(1):252.Crossref, Google Scholar
- North Carolina State Laboratory of Public Health (NCLPH) (2016) Newborn screening: Reporting - cystic fibrosis. Accessed June 2020. https://slph.ncpublichealth.com/newborn/Reporting.asp.Google Scholar
- (2014) Cost effectiveness of newborn screening for cystic fibrosis: A simulation study. J. Cyst. Fibros. 13(3):267–274.Crossref, Google Scholar
- (1994) The use of a square array scheme in blood testing. Stat. Med. 13(22):2337–2343.Crossref, Google Scholar
- (2020) Group testing for SARS-CoV-2 to enable rapid scale-up of testing and real-time surveillance of incidence. J. Infect. Dis. 222(6):903–909.Crossref, Google Scholar
- (2007) West Nile virus adheres to human red blood cells in whole blood. Clin. Infect. Dis. 45(2):181–186.Crossref, Google Scholar
- (2005) Assessing the cost of cystic fibrosis diagnosis and treatment. J. Pediatr. 147(3):S101–S105.Crossref, Google Scholar
- (2005) Use of pooled urine samples and automated DNA isolation to achieve improved sensitivity and cost-effectiveness of large-scale testing for Chlamydia trachomatis in pregnant women. J. Clin. Microbiol. 43(9):4684–4690.Crossref, Google Scholar
- (2020) Optimal data-driven policies for disease screening under noisy biomarker measurement. IISE Trans. 52(2):166–180.Crossref, Google Scholar
- (2020) A model-based economic evaluation of four newborn screening strategies for cystic fibrosis in Flanders, Belgium. Acta Clin. Belg. 75(3):212–220.Crossref, Google Scholar
- (2016) The spectrum of CFTR variants in nonwhite cystic fibrosis patients: implications for molecular diagnostic testing. J. Mol. Diagn. 18(1):39–50.Crossref, Google Scholar
- (2013) Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat. Genet. 45(10):1160–1167.Crossref, Google Scholar
- (2017) Markov Decision Processes for Screening and Treatment of Chronic Diseases (Springer International Publishing, Cham, Switzerland), 189–222.Crossref, Google Scholar
- (2012) Immunoreactive trypsinogen (IRT) as a biomarker for cystic fibrosis: Challenges in newborn dried blood spot screening. Mol. Genet. Metab. 106(1):1–6.Crossref, Google Scholar
- (2005) Psychosocial risk associated with newborn screening for cystic fibrosis: Parents’ experience while awaiting the sweat-test appointment. Pediatrics 115(6):1692–1703.Crossref, Google Scholar
- (2015) Linne & Ringsrud’s Clinical Laboratory Science-E-Book: The Basics and Routine Techniques (Elsevier Health Sciences, St. Louis).Google Scholar
- (2006) Cost-effectiveness of 4 neonatal screening strategies for cystic fibrosis. Pediatrics 118(3):896–905.Crossref, Google Scholar
- ; CHOPIN Study Group (2015) Cost-effectiveness of newborn screening for cystic fibrosis determined with real-life data. J. Cyst. Fibros. 14(2):194–202.Crossref, Google Scholar
- (2012) A decision-tree approach to cost comparison of newborn screening strategies for cystic fibrosis. Pediatrics 129(2):e339–e347.Crossref, Google Scholar
- (2012) Multiple positive sweat chloride tests in an infant asymptomatic for cystic fibrosis. Lab. Med. 43(2):1–5.Google Scholar
- Wisconsin State Laboratory of Hygiene (WSLH) (2018) Newborn blood screening panel of diseases: Cystic fibrosis. Accessed June 2020. http://www.slh.wisc.edu/clinical/newborn/health-care-professionals-guide/nbs-test-panel-of-diseases/#cf.Google Scholar

