Pezzolesi MG, Zbuk KM, Waite KA, Eng C. Comparative genomic and functional analyses reveal a novel cis-acting PTEN regulatory element as a highly conserved functional E-box motif deleted in Cowden syndrome. Hum Mol Genet. 2007;16:1058–71.

Article  CAS  PubMed  Google Scholar 

Chalhoub N, Baker SJ. PTEN and the PI3-kinase pathway in cancer. Annu Rev Pathol. 2009;4:127–50.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Waite KA, Eng C. Protean PTEN: form and function. Am J Hum Genet. 2002;70:829–44.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yehia L, Keel E, Eng C. The clinical spectrum of PTEN mutations. Annu Rev Med. 2020;71:103–16.

Article  CAS  PubMed  Google Scholar 

Yehia L, Eng C. 65 years of the double helix: one gene, many endocrine and metabolic syndromes: PTEN-opathies and precision medicine. Endocr Relat Cancer. 2018;25:T121–40.

Article  CAS  PubMed  Google Scholar 

Tan MH, Mester J, Peterson C, Yang Y, Chen JL, Rybicki LA, et al. A clinical scoring system for selection of patients for PTEN mutation testing is proposed on the basis of a prospective study of 3042 probands. Am J Hum Genet. 2011;88:42–56.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cummings S, Alfonso A, Hughes E, Kucera M, Mabey B, Singh N, et al. Cancer risk associated with PTEN pathogenic variants identified using multigene hereditary cancer panel testing. JCO Precis Oncol. 2023;7:e2200415.

Hendricks LAJ, Hoogerbrugge N, Venselaar H, Aretz S, Spier I, Legius E, et al. Genotype-phenotype associations in a large PTEN Hamartoma Tumor Syndrome (PHTS) patient cohort. Eur J Med Genet. 2022;65:104632.

Article  CAS  PubMed  Google Scholar 

Trost B, Thiruvahindrapuram B, Chan AJS, Engchuan W, Higginbotham EJ, Howe JL, et al. Genomic architecture of autism from comprehensive whole-genome sequence annotation. Cell. 2022;185:4409–27.e18.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42:D980–5.

Article  CAS  PubMed  Google Scholar 

Mester JL, Ghosh R, Pesaran T, Huether R, Karam R, Hruska KS, et al. Gene-specific criteria for PTEN variant curation: recommendations from the ClinGen PTEN Expert Panel. Hum Mutat. 2018;39:1581–92.

Article  PubMed  PubMed Central  Google Scholar 

Okawa Y, Iwasaki Y, Johnson TA, Ebata N, Inai C, Endo M, et al. Hereditary cancer variants and homologous recombination deficiency in biliary tract cancer. J Hepatol. 2023;78:333–42.

Article  CAS  PubMed  Google Scholar 

Momozawa Y, Iwasaki Y, Parsons MT, Kamatani Y, Takahashi A, Tamura C, et al. Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls. Nat Commun. 2018;9:4083.

Article  PubMed  PubMed Central  Google Scholar 

Fujita M, Liu X, Iwasaki Y, Terao C, Mizukami K, Kawakami E, et al. Population-based screening for hereditary colorectal cancer variants in Japan. Clin Gastroenterol Hepatol. 2022;20:2132–41.e9.

Article  CAS  PubMed  Google Scholar 

Usui Y, Taniyama Y, Endo M, Koyanagi YN, Kasugai Y, Oze I, et al. Helicobacter pylori, homologous-recombination genes, and gastric cancer. N. Engl J Med. 2023;388:1181–90.

Article  CAS  PubMed  Google Scholar 

Hirata M, Kamatani Y, Nagai A, Kiyohara Y, Ninomiya T, Tamakoshi A, et al. Cross-sectional analysis of BioBank Japan clinical data: a large cohort of 200,000 patients with 47 common diseases. J Epidemiol. 2017;27:S9–s21.

Article  PubMed  PubMed Central  Google Scholar 

Nagai A, Hirata M, Kamatani Y, Muto K, Matsuda K, Kiyohara Y, et al. Overview of the BioBank Japan project: study design and profile. J Epidemiol. 2017;27:S2–8.

Article  PubMed  PubMed Central  Google Scholar 

Buys SS, Sandbach JF, Gammon A, Patel G, Kidd J, Brown KL, et al. A study of over 35,000 women with breast cancer tested with a 25-gene panel of hereditary cancer genes. Cancer. 2017;123:1721–30.

Article  CAS  PubMed  Google Scholar 

Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, et al. A genomic mutational constraint map using variation in 76,156 human genomes. Nature 2024;625:92–100.

Article  CAS  PubMed  Google Scholar 

Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6:80–92.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, et al. Predicting splicing from primary sequence with deep learning. Cell. 2019;176:535–48.e24.

Article  CAS  PubMed  Google Scholar 

Steinhaus R, Proft S, Schuelke M, Cooper DN, Schwarz JM, Seelow D. MutationTaster2021. Nucleic Acids Res. 2021;49:W446–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hess M, Keul F, Goesele M, Hamacher K. Addressing inaccuracies in BLOSUM computation improves homology search performance. BMC Bioinforma. 2016;17:189.

Article  Google Scholar 

Mighell TL, Evans-Dutson S, O’Roak BJ. A saturation mutagenesis approach to understanding PTEN Lipid phosphatase activity and genotype-phenotype relationships. Am J Hum Genet. 2018;102:943–55.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Matreyek KA, Stephany JJ, Ahler E, Fowler DM. Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers. Genome Med. 2021;13:165.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, et al. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nat Genet. 2018;50:874–82.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ou J, Zhu LJ. trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data. Nat Methods. 2019;16:453–4.

Article  CAS  PubMed  Google Scholar 

Sato N, Tsunoda H, Nishida M, Morishita Y, Takimoto Y, Kubo T, et al. Loss of heterozygosity on 10q23.3 and mutation of the tumor suppressor gene PTEN in benign endometrial cyst of the ovary: possible sequence progression from benign endometrial cyst to endometrioid carcinoma and clear cell carcinoma of the ovary. Cancer Res. 2000;60:7052–6.

CAS  PubMed  Google Scholar 

Plamper M, Schreiner F, Gohlke B, Kionke J, Korsch E, Kirkpatrick J, et al. Thyroid disease in children and adolescents with PTEN hamartoma tumor syndrome (PHTS). Eur J Pediatr. 2018;177:429–35.

Article  PubMed  Google Scholar 

Keppler-Noreuil KM, Parker VE, Darling TN, Martinez-Agosto JA. Somatic overgrowth disorders of the PI3K/AKT/mTOR pathway & therapeutic strategies. Am J Med Genet C Semin Med Genet. 2016;172:402–21.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Govatati S, Kodati VL, Deenadayal M, Chakravarty B, Shivaji S, Bhanoori M. Mutations in the PTEN tumor gene and risk of endometriosis: a case-control study. Hum Reprod. 2014;29:324–36.

Article