{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T03:30:22Z","timestamp":1773113422527,"version":"3.50.1"},"reference-count":21,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T00:00:00Z","timestamp":1722816000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Laboratory Medicine and Pathology, Mayo Clinic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Cystic fibrosis is caused by biallelic pathogenic variants in the CFTR gene, which contains a polymorphic (TG)mTn sequence (the \u201cpoly-T\/TG tract\u201d) in intron 9. While T9 and T7 alleles are benign, T5 alleles with longer TG repeats, e.g., (TG)12T5 and (TG)13T5, are clinically significant. Thus, professional medical societies currently recommend reporting the TG repeat size when T5 is detected. Sanger sequencing is a cost-effective method of genotyping the (TG)mTn tract; however, its polymorphic length substantially complicates data analysis. We developed CFTR-TIPS, a freely available web-based software tool that infers the (TG)mTn genotype from Sanger sequencing data. This tool detects the (TG)mTn tract in the chromatograms, quantifies goodness of fit with expected patterns, and visualizes the results in a graphical user interface. It is broadly compatible with any Sanger chromatogram that contains the (TG)mTn tract \u00b1 15 bp. We evaluated CFTR-TIPS using 835 clinical samples previously analyzed in a CLIA-certified, CAP-accredited laboratory. When operated fully automatically, CFTR-TIPS achieved 99.8% concordance with our clinically validated manual workflow, while generally taking less than 10 s per sample. There were two discordant samples: one due to a co-occurring heterozygous duplication that confounded the tool and the other due to incomplete (TG)mTn tract detection in the reverse chromatogram. No clinically significant misclassifications were observed. CFTR-TIPS is a free, accurate, and rapid tool for CFTR (TG)mTn tract genotyping using cost-effective Sanger sequencing. This tool is suitable both for automated use and as an aid to manual review to enhance accuracy and reduce analysis time.<\/jats:p>","DOI":"10.3390\/ijms25158533","type":"journal-article","created":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T18:21:40Z","timestamp":1722882100000},"page":"8533","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Accurate and Automated Genotyping of the CFTR Poly-T\/TG Tract with CFTR-TIPS"],"prefix":"10.3390","volume":"25","author":[{"given":"Qiliang","family":"Ding","sequence":"first","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher D.","family":"Hofich","sequence":"additional","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tifani B.","family":"Kellogg","sequence":"additional","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rhonda K.","family":"Kuennen","sequence":"additional","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaitlin N.","family":"Paxton","sequence":"additional","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah M.","family":"Thieke","sequence":"additional","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kandelaria M.","family":"Rumilla","sequence":"additional","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1551-3215","authenticated-orcid":false,"given":"Linda","family":"Hasadsri","sequence":"additional","affiliation":[{"name":"Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.jcf.2022.01.009","article-title":"Worldwide rates of diagnosis and effective treatment for cystic fibrosis","volume":"21","author":"Guo","year":"2022","journal-title":"J. Cyst. Fibros."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1002\/ame2.12180","article-title":"A review of cystic fibrosis: Basic and clinical aspects","volume":"4","author":"Chen","year":"2021","journal-title":"Anim. Models Exp. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1002\/ppul.25733","article-title":"Increasing life expectancy in cystic fibrosis: Advances and challenges","volume":"57","author":"McBennett","year":"2022","journal-title":"Pediatr. Pulmonol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.jcf.2015.09.002","article-title":"Causes of death in French cystic fibrosis patients: The need for improvement in transplantation referral strategies!","volume":"15","author":"Martin","year":"2016","journal-title":"J. Cyst. Fibros."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1097\/MPA.0000000000001350","article-title":"Acute Recurrent and Chronic Pancreatitis as Initial Manifestations of Cystic Fibrosis and Cystic Fibrosis Transmembrane Conductance Regulator-Related Disorders","volume":"48","author":"Baldwin","year":"2019","journal-title":"Pancreas"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1111\/andr.12450","article-title":"Congenital bilateral absence of the vas deferens as an atypical form of cystic fibrosis: Reproductive implications and genetic counseling","volume":"6","author":"Faucz","year":"2018","journal-title":"Andrology"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1097\/01.GIM.0000139510.00644.F7","article-title":"Premarital and prenatal screening for cystic fibrosis: Experience in the Ashkenazi Jewish population","volume":"6","author":"Kornreich","year":"2004","journal-title":"Genet. Med."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Committee on Genetics (2017). Committee Opinion No. 691: Carrier Screening for Genetic Conditions. Obstet. Gynecol., 129, e41\u2013e55.","DOI":"10.1097\/AOG.0000000000001952"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1002\/humu.24250","article-title":"Elucidating clinical phenotypic variability associated with the polyT tract and TG repeats in CFTR","volume":"42","author":"Nykamp","year":"2021","journal-title":"Hum. Mutat."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1016\/j.ajhg.2023.06.002","article-title":"Using the ACMG\/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup","volume":"110","author":"Walker","year":"2023","journal-title":"Am. J. Hum. Genet."},{"key":"ref_11","first-page":"87","article-title":"The molecular basis of partial penetrance of splicing mutations in cystic fibrosis","volume":"60","author":"Kerem","year":"1997","journal-title":"Am. J. Hum. Genet."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1093\/hmg\/8.13.2339","article-title":"Functional analysis of cis-acting elements regulating the alternative splicing of human CFTR exon 9","volume":"8","author":"Niksic","year":"1999","journal-title":"Hum. Mol. Genet."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3504","DOI":"10.1073\/pnas.0400182101","article-title":"A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing","volume":"101","author":"Hefferon","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1038\/aja.2012.43","article-title":"The CFTR polymorphisms poly-T, TG-repeats and M470V in Chinese males with congenital bilateral absence of the vas deferens","volume":"14","author":"Ni","year":"2012","journal-title":"Asian J. Androl."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1038\/ng1193-274","article-title":"A mutation in CFTR produces different phenotypes depending on chromosomal background","volume":"5","author":"Kiesewetter","year":"1993","journal-title":"Nat. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"100867","DOI":"10.1016\/j.gim.2023.100867","article-title":"Updated recommendations for CFTR carrier screening: A position statement of the American College of Medical Genetics and Genomics (ACMG)","volume":"25","author":"Deignan","year":"2023","journal-title":"Genet. Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1038\/s41436-020-0822-5","article-title":"CFTR variant testing: A technical standard of the American College of Medical Genetics and Genomics (ACMG)","volume":"22","author":"Deignan","year":"2020","journal-title":"Genet. Med."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1542\/peds.2015-0811","article-title":"Newborn Screening for Cystic Fibrosis in California","volume":"136","author":"Kharrazi","year":"2015","journal-title":"Pediatrics"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Ahting, S., N\u00e4hrlich, L., Held, I., Henn, C., Krill, A., Landwehr, K., Meister, J., N\u00e4hrig, S., Nolde, A., and Remke, K. (2023). Every CFTR variant counts\u2014Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry. J. Cyst. Fibros., in press.","DOI":"10.1016\/j.jcf.2023.10.009"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1002\/dvdy.24183","article-title":"Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products","volume":"243","author":"Hill","year":"2014","journal-title":"Dev. Dyn."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/15\/8533\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:30:16Z","timestamp":1760110216000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/15\/8533"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,5]]},"references-count":21,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2024,8]]}},"alternative-id":["ijms25158533"],"URL":"https:\/\/doi.org\/10.3390\/ijms25158533","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,5]]}}}