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Challenge Lab : ML in public health and genomics
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challengeLab-ML

Challenge Lab : ML in public health and genomics.

In this assignment, students need to predict "Gestational Age" of women based on the 7 multi-omics high-dimensional datasets as illustrated below. Train data consist of 14 women. Students will be using various machine learning or deep learning (regression) models to predict the Gestational Age of 3 women using multi-omics datasets. We will assess the performance of the students based on 1) Novelty of the algorithm (50) and 2) MAE [Mean Absolute Error] (50).

Original article

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy

Contact

email id : rintu.kutum@igib.in contact number: 7838369344

Theme

  • Expose students to challenging problems in public health.
  • Allow students to team-up and solve these problems via machine learning and deep learning models.

About

About challenge

To build ML/DL models to predict gestational age (GA) from temporal high-dimentional datasets (immunome, transcriptome, microbiome, proteome and metabolome).

About data

  • Gestational Age
  • [Cell-free RNA transcriptome] Cell-free RNA (CfRNA) was extracted from 1 mL of plasma using Plasma/SerumCirculating RNA and Exosomal Purification kit (Norgen, cat 42800) followingmanufacture instruction. The residue of DNA was digested using Baseline-ZERO DNase (Epicentre) and then cleaned by RNA Clean and Concentrator-5kit (Zymo). RNA was eluted to 12 ul in elution buffer.One half of the eluted RNA was used for sequencing library preparation us-ing SMARTer Stranded Total RNAseq-Pico Input Mammalian kit (Clontech)according to the manufacturer’s manual. Short read sequencing was performedusing the Illumina NextSeq (2×75 bp) platform to the depth of more than 10million reads per samples. The sequencing reads were mapped to human refer-ence genome (hg38) using STAR aligner. Duplicates were removed by Picardand then unique reads were quantified using htseq-count.
  • [Proteome] Blood was collected into EDTA tubes, put on ice, centrifuged within 60 min-utes, and plasma was stored at−80◦C until further processing. A first analysiswas performed in the Human Immune Monitoring Center (HIMC) at StanfordUniversity using a standard, human 62-plex kit from eBiosciences/Affymetrix(San Diego, CA) according to the manufacturer’s recommendations.
  • [Microbiome] Whole genomic DNA was extracted from each vaginal swab by means ofthe PowerSoil DNA isolation kit (MO BIO Laboratories) according to the man-ufacturer’s protocol
  • [Immunome] Whole blood samples were stimulated for 15 min with either LPS, IFNα, a cock-tail containing IL-2 and IL-6, or left unstimulated.
  • [Untargeted Metabolome] Metabolites were extracted from plasma and analyzed using a broad coverageuntargeted metabolomics platform as described previously
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