Accurate Assessment and Intervention Research on Newborn Whole Genome Sequencing and Genetic Disease Risk

Primary outcomes

1. Whole-genome sequencing data

   Time frame: After the completion of sample collection, an average of 1 year.

   Complete 30-40X whole-genome sequencing of the serum cfDNA sample according to the instructions of the DNBSEQ-T7RS High-throughput Sequencing Kit (FCL PE100) V2.0, and perform bioinformatics analysis of the sequencing data.

2. Concentration of metabolite

   Time frame: After the completion of sample collection, an average of 1 year.

   The concentration of each metabolite was analyzed and calculated using the automated targeted metabolic absolute quantification software HMQuant, independently developed by BGI.

3. Construction and sequencing of cfRNA from maternal peripheral blood

   Time frame: After the completion of sample collection, an average of 1 year.

   The library construction and quality control were performed according to the BGI PALM-seq library construction method, followed by cfRNA sequencing. The PALM-seq sequencing bioinformati

4. Whole-genome DNA methylation data

   Time frame: After the completion of sample collection, an average of 1 year.

   Combining bisulfite treatment with high-throughput sequencing technology enables the efficient and accurate mapping of whole-genome DNA methylation profiles, making it a crucial tool for epigenomics research. Based on the domestically developed DNBSEQTM sequencing technology, BGI has independently developed a novel library preparation method utilizing double-strand cyclization. This approach effectively addresses the base bias issue present in traditional methylation sequencing, allowing for rapid and efficient acquisition of authentic methylation level data.

5. Protein expression differences and functional analysis

   Time frame: After the completion of sample collection, an average of 1 year.

   Sample protein preparation: Samples were taken from -80°C, and 50 μL of each sample was treated with urea, dithiothreitol, and iodoacetamide for reduction and alkylation. Solid-phase extraction plates were used to remove high-abundance proteins, followed by the addition of trypsin for enzymatic hydrolysis. Liquid chromatography-mass spectrometry detection: After enzymatic hydrolysis, the peptides were analyzed using nanoflow-high-performance liquid chromatography-high-resolution mass spectrometry (Lumos, Thermo) in DIA (data-independent acquisition) mode for data acquisition. Data analysis: DIA-NN software was used to identify and quantify proteins from the DIA data.

6. The metagenomic data

   Time frame: After the completion of sample collection, an average of 1 year.

   Vaginal secretion DNA extraction and library sequencing: Magpure Stoll DNA KF kit was used to extract DNA from vaginal secretions; Construct a metagenomic library using the MGIEasy universal DNA library preparation kit; Use Agilent 2100 Bioanalyzer to detect the fragment range and concentration of the library. Qualified libraries were sequenced using the T1 sequencing platform according to the DNBSEQ-T7RS high-throughput sequencing kit instructions. Bioinformatics analysis of metagenomic sequencing data: The metagenomic data is first subjected to quality control of the original sequences using Trimomatic software, and then contaminated sequences are removed from the processed data using fastq_streen software, including host sequences and phix library contamination; Afterwards, the BWA aligner was used for comparison, and the human genome fragments were first removed. The microbial species composition and relative abundance were evaluated using the Metaphlan2 software.