TY  - JOUR
A1  - Bilgrav Saether, Kristine
A1  - Eisfeldt, Jesper
A1  - Bengtsson, Jesse D.
A1  - Lun, Ming Yin
A1  - Grochowski, Christopher M.
A1  - Mahmoud, Medhat
A1  - Chao, Hsiao-Tuan
A1  - Rosenfeld, Jill A.
A1  - Liu, Pengfei
A1  - Ek, Marlene
A1  - Schuy, Jakob
A1  - Ameur, Adam
A1  - Dai, Hongzheng
A1  - Undiagnosed Diseases Network
A1  - Hwang, James Paul
A1  - Sedlazeck, Fritz J.
A1  - Bi, Weimin
A1  - Marom, Ronit
A1  - Wincent, Josephine
A1  - Nordgren, Ann
A1  - Carvalho, Claudia M.B.
A1  - Lindstrand, Anna
T1  - Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
Y1  - 2024/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1785 
EP  - 1797 
DO  - 10.1101/gr.279346.124 
VL  - 34 
IS  - 11 
UR  - http://genome.cshlp.org/content/34/11/1785.abstract 
N2  - Chromosomal inversions (INVs) are particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage-sensitive genes in cis. Short-read genome sequencing (srGS) can only resolve ∼70% of cytogenetically visible inversions referred to clinical diagnostic laboratories, likely due to breakpoints in repetitive regions. Here, we study 12 inversions by long-read genome sequencing (lrGS) (n = 9) or srGS (n = 3) and resolve nine of them. In four cases, the inversion breakpoint region was missing from at least one of the human reference genomes (GRCh37, GRCh38, T2T-CHM13) and a reference agnostic analysis was needed. One of these cases, an INV9 mappable only in de novo assembled lrGS data using T2T-CHM13 disrupts EHMT1 consistent with a Mendelian diagnosis (Kleefstra syndrome 1; MIM#610253). Next, by pairwise comparison between T2T-CHM13, GRCh37, and GRCh38, as well as the chimpanzee and bonobo, we show that hundreds of megabases of sequence are missing from at least one human reference, highlighting that primate genomes contribute to genomic diversity. Aligning population genomic data to these regions indicated that these regions are variable between individuals. Our analysis emphasizes that T2T-CHM13 is necessary to maximize the value of lrGS for optimal inversion detection in clinical diagnostics. These results highlight the importance of leveraging diverse and comprehensive reference genomes to resolve unsolved molecular cases in rare diseases. 
ER  -