Concurrent exome-targeted next-generation sequencing and single nucleotide polymorphism array to identify the causative genetic aberrations of isolated Mayer-Rokitansky-Küster-Hauser syndrome.
OBJECTIVE
Can the use of whole-exome sequencing (WES) together with single nucleotide polymorphism (SNP) array help to identify novel causative genes of isolated Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome?


CONCLUSIONS
OR4M2 (olfactory receptor, family 4, subfamily M, member 2) and PDE11A (phosphodiesterase 11A) gene loss-of-function variants as well as deletions at 15q11.2, 19q13.31, 1p36.21, and 1q44 were identified as possible commonly altered regions in patients with type 1 MRKH.


BACKGROUND
The isolated form of Müllerian aplasia is the most common subtype of MRKH syndrome, which invariably leads to difficulties producing offspring in affected women. However, there is little information currently available to allow for genetic testing and counseling to be performed for those affected by this syndrome.


METHODS
This was a case-series genetic study. A total of seven consecutive unrelated women with type 1 MRKH were enrolled. The enrollment and experimental procedures were performed over a 2-year period.


METHODS
Whole exome-targeted next-generation sequencing and SNP array (Affymetrix Genome-Wide Human SNP Array 6.0) were performed on the first five unrelated women with type 1 MRKH syndrome. The data were combined, and the '3-hit principal' was applied on a genome-wide scale to search for the common causative genes. Quantitative PCR (qPCR) and Sanger sequencing were used to validate the identified genomic copy number losses and variants. Replication tests using direct Sanger sequencing and qPCR were performed on the remaining two women with type 1 MRKH syndrome to support the credibility of the potential candidate genes and deletions.


RESULTS
A total of 3443 damaging variants based on WES were shown to intersect with 1336 copy number variations (deletions) derived from the SNP array. Four highly recurrent deletions at 15q11.2 (80%), 19q13.31 (40%), 1p36.21 (40%) and 1q44 (40%) were identified in the first five women with type 1 MRKH syndrome and were considered to be novel candidate aberrations. A previously reported 1q21.1 deletion was also recurrent in two of the first five women with type 1 MRKH syndrome. The 1q44 and 19q13.31 deletions were present in at least one of the two additional patients. Damaging variants were detected in HNRNPCL1 (heterogeneous nuclear ribonucleoprotein C-like 1), OR2T2 (olfactory receptor, family 2, subfamily T, member 2), OR4M2, ZNF816 (zinc finger protein 816), and PDE11A in several of the initial five patients. Among these, the damaging variants of OR4M2 (located at 15q11.2) and PDE11A were found in at least one of the two additional patients with type 1 MRKH.


CONCLUSIONS
In this study, we only searched for the deletions or damaging variants causing loss-of-function of genes in at least three of the initial five patients (3-hit criteria). Therefore, the study was designed to only detect common causative genes. Genomic duplications and/or rare individual mutations that may have also contributed to MRKH syndrome were not investigated.


CONCLUSIONS
This study demonstrated the feasibility of the use of combined data from both WES and SNP arrays for the identification of possible common causative genetic aberrations in patients with type 1 MRKH syndrome on a genome-wide scale. Further validation of our found causative genes is required before applying on genetic testing and counseling.


BACKGROUND
The study was supported by grants from the National Science Council of Taiwan (NSC98-2314-B002-105-MY3 and NSC 100-2314-B002-027-MY3). The funding sources had no involvement in the design or analysis of the study. The authors have no competing interests to declare.


BACKGROUND
Not applicable.
Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan.
Mei-Jou
MJ
Chen
Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan.
Shin-Yi
SY
Wei
Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 100, Taiwan.
Wei-Shiung
WS
Yang
Graduate Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
Tsai-Tzu
TT
Wu
Department of Medical Genetics, National Taiwan University Hospital, Taipei 100, Taiwan.
Huei-Ying
HY
Li
Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan.
Hong-Nerng
HN
Ho
Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan.
Yu-Shih
YS
Yang
Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 100, Taiwan Department of Medical Genetics, National Taiwan University Hospital, Taipei 100, Taiwan Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei 100, Taiwan paylong@ntu.edu.tw.
Pei-Lung
PL
Chen
D058489:46, XX Disorders of Sex Development / Q000235:genetics*; D000328:Adult; D000013:Congenital Abnormalities / Q000235:genetics*; D059472:Exome / Q000235:genetics*; D005260:Female; D017353:Gene Deletion; D006801:Humans; D009095:Mullerian Ducts / Q000002:abnormalities*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
Mayer–Rokitansky–Küster–Hauser syndrome; Müllerian aplasia; next-generation sequencing; single nucleotide polymorphism array; whole-exome sequencing