Responses to Questions.pdf

Responses to Questions

HHS-NIH-NIDA-CSS-75N95022Q00002

1. Question: Do you have a list of targets to be analyzed? We would need to work with Illumina on designing this custom array.

Response: The statement of work lists the targets to be analyzed on page 2, line 1 as follows:

“This custom beadchip is the Infinium Global Screening Array-24 v3.0 BeadChip (GSA MD version 3), as described at http://glimdna.org/global-screening-array.html.” Clicking on the provided link (http://glimdna.org/global-screening-array.html) will open a webpage. On this webpage, there is a link to the SNP list that is contained on the GSA MD version 3. Clicking on the link will download the list of SNPs to the vendor’s computer.

2. Question: What type of samples (tissue, cell or other type) need to be genotyping?

Response: The samples to be genotyped consist of blood samples taken from humans diagnosed with Guillain-Barre syndrome.

3. Question: What’s the amount of sample material for each sample?

Response: The standard sample amount is one to three milliliters of blood.

4. Question: Would all samples be provided at once, or in batches of specified number of samples at some pre-set schedule?

Response: The samples are currently located at the Erasmus University. The samples cannot be shipped outside of the European Union (EU), due to EU, Dutch and Erasmus University regulations.

5. Question: How do we transport the samples? Will the government mail the sample to the vendor lab? Or the vendor need to pick them up?

Response: The samples are currently located at the Erasmus University. The samples cannot be shipped outside of the EU, due to EU, Dutch and Erasmus University regulations.

6. Question: Do you expect that significant number of samples will not pass the quantity / quality acceptance criteria for genotyping?

Response: NIA expects all of the samples to pass the quantity and quality acceptance criteria for genotyping.

7. Question: In regards to the iselect array highlighted above, will the vendor be responsible for furnishing the array?

Response: Yes, vendor is responsible for furnishing the array

8. Question: If the vendor is responsible for the array, can you provide how much content will be needed on the array? Will vendor be responsible for designing the custom array?

http://glimdna.org/global-screening-array.html http://glimdna.org/global-screening-array.html

Response: No, vendor will not design the array. Government will assist with array specifications. Please note vendor is responsible for providing the 1080 proprietary samples owned by Erasmus MC of Rotterdam.

9. Question: Can you inform on how many proposed SNP’s there will be on the design for the array?

Response: Approximately 650,000 SNPS.

10. Question: When you say vendor is responsible for providing the 1,080 samples from Erasmus, do you mean extracting these sample?

Response: Vendor awarded this contract is responsible for contacting Erasmus MC of Rotterdam, obtaining the proprietary 1080 Guillain-Barré syndrome samples directly from Erasmus MC of Rotterdam, extracting DNA from those samples, checking quality and quantity and performing Genome Wide Association Study analysis of the samples.

11. Question: Would it be possible to extend the deadline with 1-2 weeks so that our lawyers have more time to go through all terms and conditions?

Response: Yes

12. Question: If I understood it correctly, we need to send a quote and we need to fill in the two forms regarding telecommunications. Is that right or do you expect more documents from our side?

Response: Yes, you will need to complete the telecommunication forms.

13. Question: Second, the EU law does not allow us to send genotype data on an individual level (‘raw data’ mentioned in the SOW). Would it be possible to adapt the SOW on this?

Response: Minor allele frequencies and association analysis results for the 1080 samples.

14. Question: In addition, the term of 4 weeks is much too tight, since we need to extract DNA too and we depend on other laboratories in our institute. A term of 26 weeks should be doable.

Response: Yes and extension will be granted