![](media/image1.jpeg){width="7.5in"
height="0.6666666666666666in"}**[CGF Pre-Genotyping QC
Report]{.underline}**

The Pre-genotyping QC report is provided to investigators at the
conclusion of sample handling activities and after the samples have been
reviewed by CGF QC personnel in advance of inclusion in a GRC approved
genotyping project. It is designed to give investigators an opportunity
to review the exact composition of their genotyping project before such
genotyping actually occurs. This information should be reviewed by the
investigator or designee at the time of report receipt.

***Any requests to adjust project composition or requests to delay the
genotyping project must be made within seven calendar days of report
receipt. In absence of alternate directions for the investigator, CGF
will continue the genotyping project with the reported sample list.***

The Pre-genotyping QC report is automatically generated by the CGF LIMS
and is composed of five pages:

**Summary:** Contains project details and overall QC results.

**Sample Status:** Contains results of pre-genotyping QC on a sample
level.

**NanoDrop Failure Data:** Contains details on samples that failed
initial CGF qualification (\< 25 ng/ul after volume normalized \>=
50ul).

**Identifiler Data:** Contains sample profiling data used for
concordance checks.

**Picogreen Data:** Contains Picogreen quantitation measurement of
(double stranded) dsDNA.

Below is a description of each field that may be found in the four data
pages of this report. Although some of the information is repetitive
between pages, it is included here in total for ease of data review.

[Page: Sample Status]{.underline}

  ------------------------- ---------------------------------------------
  Sample/Presample ID       Internal, unique ID assigned by CGF LIMS

  Customer Sample ID        Vial ID of sample as provided in electronic
                            shipping manifest from the sender of the
                            material

  Receipt ID                Internal CGF identifier of unique receipt
                            (shipment) of samples within a study

  Status                    Result of pre-genotyping QC; see details
                            below

  Notes                     When available, notes for clarification of
                            sample exclusion reason
  ------------------------- ---------------------------------------------

[Page: NanoDrop Failure Data]{.underline}

  ------------------------- ---------------------------------------------
  PreSample ID              Internal, unique ID assigned by CGF LIMS

  Customer Sample ID        Vial ID of sample as provided in electronic
                            shipping manifest from the sender of the
                            material

  Receipt ID                Internal CGF identifier of unique receipt
                            (shipment) of samples within a study

  Status                    Fail CGF QC; denotes concentration less than
                            25 ng/ul

  Expected Concentration    Concentration of sample as provided in
  (ng/ul)                   electronic shipping manifest

  Actual Concentration      Concentration of sample as obtained by CGF
  (ng/ul)                   NanoDrop SOP (after q.s.to 50 ul if
                            necessary).
  ------------------------- ---------------------------------------------

[Page: Identifiler Data]{.underline}

  ------------------------- ---------------------------------------------
  Customer Sample ID        Vial ID of sample as provided in electronic
                            shipping manifest from the sender of the
                            material

  CGF Sample ID             Internal, unique ID for a sample that has
                            passed the NanoDrop requirements, assigned by
                            CGF LIMS

  Notes                     Details on results; see below for additional
                            information
  ------------------------- ---------------------------------------------

[Page: Picogreen Data]{.underline}

  ------------------------- ---------------------------------------------
  CGF Sample ID             Internal, unique ID for a sample that has
                            passed the NanoDrop requirements, assigned by
                            CGF LIMS

  Customer Sample ID        Vial ID of sample as provided in electronic
                            shipping manifest from the sender of the
                            material

  Receipt ID                Internal CGF identifier of unique receipt
                            (shipment) of samples within a study

  Picogreen Amount (ng)     Total current yield of sample as determined
                            by CGF Picogreen SOP

  Volume (ul)               Total current volume of sample at time of
                            Picogreen assay

  Picogreen Concentration   Concentration of sample as obtained by CGF
  (ng/ul)                   Picogreen SOP
  ------------------------- ---------------------------------------------

**[Additional information on Identifiler notes:]{.underline}**

Samples that performed poorly in the Identifier assay may have the
following notes associated:

*Size Standard Failure* - The internal lane size standard did not yield
the expected results and therefore sample data cannot be analyzed
accurately.

*Low* - The sample did not yield genotypes over 200 RFUs in more than 2
of the 16 markers.

*Contaminated* - The sample shows evidence of contamination as more than
2 genotypes are found in more than 2 of the 16 markers.

*3 alleles observed at (marker name): #, #, \#* - The sample yields 3
genotypes of equal RFUs, at one marker only, which cannot be attributed
to contamination, bleed-through of another dye, spectral pull-up, or
incomplete 3\' nucleotide addition.

All samples with these performance issues may be repeated in order to
confirm contamination or to collect the information required for a full
QC review. However, if a sample fails to produce useable Identifiler
results, it is not eliminated from project inclusion (the sample may
still be eliminated for other reasons e.g. Insufficient DNA).
Contaminated samples will always be excluded from genotyping projects.

**[Pre-genotyping QC status descriptions:]{.underline}**

*Fail CGF QC* - Sample failed initial NanoDrop requirements of 50 ul at
25 ng/ul as outlined in the CGF current rules for sample receipt (may be
found at: <http://cgf.nci.nih.gov/docs/sample_receipt.pdf>).

*Gender Discordance* - Sex of sample as defined by Amelogenin marker is
discordant with reported gender from investigator.

*Include* - Sample passed all QC criteria and will be genotyped for this
project.

*Insufficient DNA* - Insufficient sample for this project (platform and
project dependant).

*Matched Pair Failure* - Sample not required as its matched pair failed
QC criteria.

*Not Received* - Sample not received at CGF although included in
electronic manifest.

*Other* - (This exclude reason will be supported by notes.)

*Partial Plate* - Physical limitation of platform (platform dependant);
reduces excessive waste

*PI Exclude* - PI request to exclude samples; more detail may be
available in notes.

*Previously Genotyped* - Sample already genotyped on requested SNPs
within a different project.

*Profiling Discordance* - Discordance between subject ID and sample
genetic identity as determined by Identifiler assay.

*Redundant nonQC* - Excessive subject samples not required for
completion of project.

*Redundant QC* - Excessive QC samples not required for completion of
project.

*Sample Contamination* - Presence of multiple DNA donors as determined
by Identifiler assay.