Long-read genome and RNA sequencing resolve a pathogenic intronic germline LINE-1 insertion in APC

Alexandra A Baumann; Lisanne I Knol; Marie Arlt; Tim Hutschenreiter; Anja Richter; Thomas J Widmann; Marcus Franke; Karl Hackmann; Sylke Winkler; Daniela Richter; Isabel Spier; Stefan Aretz; Daniela Aust; Joseph Porrmann; Doreen William; Evelin Schröck; Hanno Glimm; Arne Jahn

doi:10.1038/s41525-025-00485-5

Long-read genome and RNA sequencing resolve a pathogenic intronic germline LINE-1 insertion in APC

NPJ Genom Med. 2025 Apr 4;10(1):30. doi: 10.1038/s41525-025-00485-5.

Authors

Alexandra A Baumann^#^{1

2

3}, Lisanne I Knol^#^{2

4

5}, Marie Arlt^{1

3}, Tim Hutschenreiter^{1

3}, Anja Richter^{1

2

3}, Thomas J Widmann^{2

6}, Marcus Franke^{1

3}, Karl Hackmann^{1

3}, Sylke Winkler⁷, Daniela Richter^{2

4

5

8

9}, Isabel Spier^{10

11}, Stefan Aretz^{10

11}, Daniela Aust^{12

13}, Joseph Porrmann^{1

3}, Doreen William^{1

3}, Evelin Schröck^{1

2

3

7

8

9}, Hanno Glimm^{2

4

5

8

9

14

15}, Arne Jahn^{16

17

18

19

20}

Affiliations

¹ Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany.
² National Center for Tumor Diseases (NCT), NCT/UCC Dresden,, a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.
³ ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany.
⁴ Department of Translational Medical Oncology, NCT Dresden and DKFZ, Dresden, Germany.
⁵ Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
⁶ Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), PTS Granada, managed by Fundación Pública Andaluza Progreso y Salud (FPS), Granada, Spain.
⁷ Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
⁸ German Cancer Consortium (DKTK), Dresden, Germany.
⁹ German Cancer Research Center (DKFZ), Heidelberg, Germany.
¹⁰ Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany.
¹¹ National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.
¹² Institute of Pathology, University Hospital Carl Gustav Carus at TUD Dresden University, Dresden, Germany.
¹³ Tumor- and Normal Tissue Bank of the University Cancer Center (UCC), University Hospital Carl Gustav Carus, Medical Faculty, TUD Dresden University of Technology, Dresden, Germany.
¹⁴ Center for Personalized Oncology, NCT Dresden and University Hospital Carl Gustav Carus, Faculty of Medicine and TUD Dresden University of Technology, Dresden, Germany.
¹⁵ Translational Functional Cancer Genomics, NCT Heidelberg and DKFZ, Heidelberg, Germany.
¹⁶ Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany. Arne.Jahn@ukdd.de.
¹⁷ National Center for Tumor Diseases (NCT), NCT/UCC Dresden,, a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany. Arne.Jahn@ukdd.de.
¹⁸ ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany. Arne.Jahn@ukdd.de.
¹⁹ German Cancer Consortium (DKTK), Dresden, Germany. Arne.Jahn@ukdd.de.
²⁰ German Cancer Research Center (DKFZ), Heidelberg, Germany. Arne.Jahn@ukdd.de.

^# Contributed equally.

Abstract

Familial adenomatous polyposis (FAP) is caused by pathogenic germline variants in the tumor suppressor gene APC. Confirmation of diagnosis was not achieved by cancer gene panel and exome sequencing or custom array-CGH in a family with suspected FAP across five generations. Long-read genome sequencing (PacBio), short-read genome sequencing (Illumina), short-read RNA sequencing, and further validations were performed in different tissues of multiple family members. Long-read genome sequencing resolved a 6 kb full-length intronic insertion of a heterozygous LINE-1 element between exons 7 and 8 of APC that could be detected but not fully resolved by short-read genome sequencing. Targeted RNA analysis revealed aberrant splicing resulting in the formation of a pseudo-exon with a premature stop codon. The variant segregated with the phenotype in several family members allowing its evaluation as likely pathogenic. This study supports the utility of long-read DNA sequencing and complementary RNA approaches to tackle unsolved cases of hereditary disease.