FAQ

Frequently asked questions

When will I know the result?

The successful applicant for the research grant will be announced on August 12th , 2019. The result

will also be announced by email and on the Illumina’s Social Media.

 

 

Will Illumina or MLL commercialize any discoveries resulting from the research conducted using this grant?

No, Illumina and MLL will only be granted rights to promote the utilization of Illumina’s methods and

technologies resulting from the research for the marketing of Illumina’s products.

 

 

Am I eligible to apply as a research employee of a private company?

Yes, employees of private companies are eligible as well.

 

 

May I apply for the grant multiple times with different projects?

Unfortunately, each individual may apply for the grant with one project only.

 

 

Is the research grant only limited to projects on human research?

Yes, the grant is limited to human research only.

 

How many ng of DNA is required for WGS provided in this grant?

For DNA library preparation either TruSeq PCR free or Nano protocols will be used. In case of TruSeq PCR Free library preparation, minimum 1µg of DNA is required. For TruSeq Nano DNA protocol 100ng are sufficient.

 

What is the preferred method for DNA quantification?

ANy standard DNA quantification method is acceptable. There will be a quality check performed at MLL.

 

How many ng of RNA is required for RNA Seq?

Minimum 250ng with a RIIN > 7

 

What is the preferred method to estimate the quality of RNA?

Any standard of RNA quantification including RIN calculation can be used. A quality check will be performed at MLL.

Can we accept the projects with tumour DNA derived from formalin fixed paraffin embedded tissue?

Unfortunately no, FFPE samples will not be accepted.

 

Which bioinformatics pipeline is going to be used for data analysis?

Primary and secondary data analysis will be performed on BaseSpace Sequence Hub ( BSSH) using the latest version of WGS, Tumor Normal and RNA-seq Apps as described here: https://www.illumina.com/products/by-type/informatics-products/basespace-sequence- hub/apps.html.

Any tertiary analysis will be performed upon request using tools and methodology developed by MLL either in BSSH or on computational servers chosen by MLL.

 

In which format will the results be provided in?

The results will be provided either as FASTQ.gz files (see delivery method below) or individually or as a bundle of the standard files produced by the corresponding BSSH Apps: WGS + Tumor Normal, RNA-Seq. For instance, for WGS: BAM, VCF, gVCF, Structural variants and CNVs, somatic VCF sample metrics and sample reports, and corresponding files produced by RNA-Seq Alignment App. The complete list of the output files can be viewed on corresponding App Data sheets as referenced here: https://www.illumina.com/products/by-type/informatics-products/basespace-sequence- hub/apps.html.

Any tertiary analysis (e.g. variant interpretation or any report of the significance of discovered variants) shall be provided by MLL upon request, using tools and methodology developed by MLL.

 

Where sequencing results (data) are going to be stored?

All sequencing data will be stored in BaseSpace Sequence Hub (BSSH) in Frankfurt on MLL domain for period of analyses, after this the data have to be downloaded by participants to the storage of

 

their choice. MLL will retain data in BSSH Frankfort for the period of 30 days after analysis has been completed.

 

 

How will my results (data) be delivered?

Results will be delivered via Base Space Sequence Hub (BSSH) by transferring data to the

participants’ personal BSSH account or by means of providing a download link from BSSH or by other means if specifically agreed with MLL or Illumina.

 

 

What is your policy of data retention after I receive my results?

Once results of the analysis are delivered to the participants in the format agreed and described above, all sequencing data (raw bcl files, fastq files and all analysis files) will be deleted within 30 days from BSSH Frankfurt and MLL servers if applicable. It is the participants responsibility to maintain and archive data by their own means unless specifically agreed with MLL or Illumina.

 

 

How long will it take before I receive my results?

Four weeks from the arrival of all samples.

 

For Research Use Only. Not for use in diagnostic procedures.

 

 

When will I know the result?

The successful applicant for the research grant will be announced on August 12th , 2019. The result

will also be announced by email and on the Illumina’s Social Media.

 

Will Illumina or MLL commercialize any discoveries resulting from the research conducted using this grant?

No, Illumina and MLL will only be granted rights to promote the utilization of Illumina’s methods and

technologies resulting from the research for the marketing of Illumina’s products.

 

Am I eligible to apply as a research employee of a private company?

Yes, employees of private companies are eligible as well.

 

May I apply for the grant multiple times with different projects?

Unfortunately, each individual may apply for the grant with one project only.

 

Is the research grant only limited to projects on human research?

Yes, the grant is limited to human research only.

 

Which bioinformatics pipeline is going to be used for data analysis?

Primary and secondary data analysis will be performed on BaseSpace Sequence Hub ( BSSH) using the latest version of WGS, Tumor Normal and RNA-seq Apps as described here:

https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps.html

Any tertiary analysis will be performed upon request using tools and methodology developed by MLL either in BSSH or on computational servers chosen by MLL.

 

In which format will the results be provided in?

The results will be provided either as FASTQ.gz files (see delivery method below) or individually or as a bundle of the standard files produced by the corresponding BSSH Apps: WGS + Tumor Normal, RNA-Seq. For instance, for WGS: BAM, VCF, gVCF, Structural variants and CNVs, somatic VCF sample metrics and sample reports, and corresponding files produced by RNA-Seq Alignment App. The complete list of the output files can be viewed on corresponding App Data sheets as referenced here: https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps.html

Any tertiary analysis (e.g. variant interpretation or any report of the significance of discovered variants) shall be provided by MLL upon request, using tools and methodology developed by MLL.

 

Where sequencing results (data) are going to be stored?

All sequencing data will be stored in BaseSpace Sequence Hub (BSSH) in Frankfurt on MLL domain for period of analyses, after this the data have to be downloaded by participants to the storage of

their choice. MLL will retain data in BSSH Frankfort for the period of 30 days after analysis has been completed.

 

How will my results (data) be delivered?

Results will be delivered via Base Space Sequence Hub (BSSH) by transferring data to the

participants’ personal BSSH account or by means of providing a download link from BSSH or by other means if specifically agreed with MLL or Illumina.

 

What is your policy of data retention after I receive my results?

Once results of the analysis are delivered to the participants in the format agreed and described above, all sequencing data (raw bcl files, fastq files and all analysis files) will be deleted within 30 days from BSSH Frankfurt and MLL servers if applicable. It is the participants responsibility to maintain and archive data by their own means unless specifically agreed with MLL or Illumina.

 

How long will it take before I receive my results?

Four weeks from the arrival of all samples.

 

For Research Use Only. Not for use in diagnostic procedures.