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Experience in developing the human genome standard E701.

Iuliia Vasiliadis1, Vera Belova1, Anna Shmitko1

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The first Russian human genome standard, E701, was created for genomic data quality control. This standard provides millions of validated genomic variants for accurate sequencing analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Human Genetics

Background:

  • Accurate human genome analysis relies on high-quality reference standards.
  • The development of a national human genome standard is crucial for advancing genomic research and clinical applications in Russia.

Purpose of the Study:

  • To establish the first Russian human genome standard, E701.
  • To characterize the genomic variants within the E701 standard for quality control in sequencing data analysis.

Main Methods:

  • Whole-genome sequencing (WGS) using MGI Tech and Illumina platforms.
  • Alignment to the human genome reference GRCh38.p14 and variant calling.
  • Whole-exome sequencing (WES) with multiple enrichment panels for concordance analysis.
  • Mitochondrial DNA sequencing with high coverage.

Main Results:

  • Identification of 3,842,877 genomic variants in the E701 sample.
  • Filtering by GIAB high-confidence regions yielded 3,262,154 variants.
  • Discovery of 9,096 bi-allelic variants on autosomes and X chromosome (MAF > 0.4).
  • Mitochondrial DNA sequencing achieved >99.9% coverage at 1000×.

Conclusions:

  • The E701 standard provides a robust set of genomic variants for statistical quality metric calculation.
  • This standard facilitates accurate and reliable human genome analysis in Russia.
  • The comprehensive characterization supports its use in diverse genomic applications.