B-213 Including Turner Syndrome Screening in Newborn Sequencing by Using NGS Read Counts to Infer Sex Chromosomes Copy Number: Leveraging Existing Data to Enhance Early Diagnosis
Authors: Barra G , Correia S , Coqueiro A , Mesquita P , Benício R , Pessoa N , Sgardioli I , Lamas A , Andrade A , Martins G , Jácomo R , Nery L 
Published: October 2024

Abstract

Background
Turner Syndrome (TS) can lead to heart defects, short stature, and premature ovarian failure. Early diagnosis can improve outcomes, but routine screening is not standard, often delaying diagnosis until symptoms prompt karyotype analysis. Newborn NGS sequencing offers potential for early detection of genetic disorders and targets numerous gene regions on autosomes and sex chromosomes. It could be utilized to deduce sexual chromosomal copy number variations, including not only chrX monosomy but also its partial deletions and structural alterations, and chrY, which increases the risk of gonadoblastoma in TS patients. Thus, this study aims to validate a TS screening approach using NGS read count data from newborn sequencing to develop a strategy for early detection.

Methods
DNA samples with established chromosomal microarray ChrX and ChrY copy-number assessments were used. The cohort included 13 males (46,XY), 10 females (46,XX), 5 TS cases (45,X), 5 mosaic TS cases (2 with chrY, 3 without), 1 TS case with Isochromosome Xq, 8 Klinefelter Syndrome cases (47,XXY), and one case (48,XXYY). For NGS, a focused newborn sequencing panel targeting 388 genes derived from the larger xGEN Inherited Disease Panel (Integrated DNA Technologies) was employed. The larger panel covers 2,968 chrX regions, 53,455 autosomal regions, and 135 chrY regions. Sample processing utilized the xGEN DNA Library Prep and Hybridization Capture (Integrated DNA Technologies) and sequencing on NextSeq-500 (Illumina). The alignment was conducted with Dragen Enrichment v.3.9.5 and read count analysis with Samtools v.1.19.2. ChrX and ChrY copy numbers were assessed by comparing chrX and chrY read count ratios to autosomal read counts. Hierarchical clustering grouped samples based on ratio similarities, aiding result attribution. To identify structural alterations in each arm of chrX, every tested chrX region was analyzed for read count ratio calculation and subjected to circular binary segmentation using the DNAcopy R package. The observed sex chromosome counts were compared to expected results to validate the approach.

Results
Observed chrX/autosome and chrY/autosome ratio ranges matched the expected sex chromosome counts: 0.99-1.03 and 0.82-1.02 for 46,XY; 1.92-1.97 and 0.00-0.01 for 46,XX; 1.00-1.02 and 0.00-0.00 for 45,X; 1.15-1.46 and 0.00-0.00 for mosaic TS without chrY; 0.98-1.06 and 0.27-0.32 for mosaic TS with chrY; 2.45 and 0.0 for TS with Isochromosome Xq; 1.82-2.01 and 0.87-0.95 for 47,XXY; and 2.02 and 1.96 for 48,XXYY. Hierarchical cluster analysis grouped these values into three branches: one for 48,XXYY, one for 47,XXY, 46,XX, and Isochromosome Xq, and one for all other TS samples and 46,XY. TS and 47,XXY samples were further divided into subbranches from 46,XX and 46,XY. Circular binary segmentation of chrX read counts provided a visual profile of the copy number for each arm of chrX, explaining structural alterations in out-of-pattern chrX dosages, such as 2.45, 1.15, and 1.46.

Conclusions
There was complete agreement between the NGS read count-based assessment of sex chromosome copy number and the expected results for 46,XY, 46,XX, 45,X, TS with mosaic and structural variants, 47,XXY, and 48,XXYY samples. This suggests that TS can be effectively screened using newborn sequencing NGS data.