1211532_Q&A.docx

Amendment 0001 to Solicitation FDA_SOL_1211532:

The purpose of this amendment is as follows:

1. Post Answers to Questions received by June 17, 2019 at 2:00pm Central Time. Answers have been provided by the technical point of contact for this requirement:

Q: For CMap data analysis, are there particular end points you are looking for?

A: CMAP data analysis and endpoint description:

Based on the miRNA-seq data, the Connectivity Map, or CMap shall be used as a resource to probe relationships between diseases, cell physiology, and therapeutics. The changes in gene expression, or “signatures,” that arise from a disease, genetic perturbation (knockdown or overexpression of a gene) or treatment with a small molecule shall be compared for similarity to all perturbational signatures in the database. Gene pathways related with miRNA transcriptional effects and physiological effects shall also be analyzed using CMap and gene interaction networks shall be generated illustrating the functional relationship of selected miRNA molecules.

Q: Likewise, for co-variant and multi regression analysis, are there particular end points you are looking for?

A: For co-variant and multi regression analysis comparison between groups:

After quality control and normalization procedure, differentially expressed miRNAs and their potential mRNA targets (or transcript) shall be further analyzed by Limma package in R while adjusting for all potential covariates. Multiple testing shall bef controlled by Benjamini-Hochberg Procedure. For example, the expression values of specific transcript (microRNA) shall be formulated by linear model as y=C+D+T+CD+CT+DT+CDT (C: Chemical, D: dose, T: time, CD, CT,DT, represent interaction between two of them. CDT, interaction among three variables).

When testing between dose groups adjusted on two factors, more potential covariates shall be able to be added in the linear model.

(End of Amendment 0001 to Solicitation FDA_SOL_1511532)