Change QC pass limit for cfDNA samples for EPP "Calculate Amounts" in TWIST v7

[idalindegaard]

Lims Issue

For definitions of headings below see Basic Concepts.

**Work Flow:**TWIST v7
Protocol: Initial QC TWIST v3
Step: Quantit QC (DNA) TWIST v2 and Qubit QC (DNA) TWIST v2

Description: Describe issue here!!!
We will receive more and more cfDNA samples and they have a lower limit for passing the amount-check than other sample sources, which is done in steps Quantit QC (DNA) TWIST v2 and Qubit QC (DNA) TWIST v2 when running the EPP "Calculate Amounts".

The lower limit for cfDNA is 10 ng (and 25 ng for other sources).
We want the script to also take into account the "Source" udf and make sure "cfDNA" has different QC limits

[Karl-Svard]

Looks like this is already implemented in the script?

def get_qc(source: str, conc: float, amount: float) -> str:
    """QC-criteria depends on sample source, total amount and sample concentration. See AMS doc 1117, 1993 and 2125.
    The volume is subtracted by 3 in the calculations. This is beacause the lab uses 3 ul in the initial qc measurements.
    """

    qc = "FAILED"

    if source == "cfDNA":
        if amount >= 10 and conc <= 250 and conc >= 0.2:
            qc = "PASSED"
    else:
        if amount >= 250 and conc <= 250 and conc >= 8.33:
            qc = "PASSED"

    return qc

Or should we lower the threshold of normal samples from 250 to 25 ng?

[idalindegaard]

The script did not work for some cfDNA samples this week, but I saw that the sample source for cfDNA is written as "cell-free DNA", so the script needs an update (looking at the previous comment from KSV)

[Karl-Svard]

PR opened #445