Create a controlled-cross contamination log documenting post-PCR microsatellite amplification artifacts across three NGS replicates

NGS Replicate Files *

Microsatellite Panel * Select panel type CODIS STR (20 loci) PowerPlex 16 HS Investigator 24Plex Custom forensic panel (5-15 loci) Cancer microsatellite instability panel Triplet-repeat disease panel Forensic identification multiplex Research custom panel Pharmacogenetic STR markers Conservation genetics microsatellites

Contamination Source Hypothesis * Select contamination hypothesis PCR carryover from previous amplicon Cross-contamination between samples Reagent contamination (Taq polymerase/primers) Environmental laboratory contamination Index hopping in multiplex run Adapter dimer amplification artifacts Pipetting errors during setup Thermocycler well-to-well contamination Post-PCR handling contamination Multiple contamination sources suspected Unknown source - requires broad analysis

Technical Replicates Setup * Select replicate type Same DNA extract, three independent PCRs Three DNA extracts from same sample, one PCR each Same PCR product split for three library preps Three technical replicates from independent DNA isolations Same DNA extract, three barcoded libraries from same PCR Chronologically spaced PCRs (days apart) from same extract Same PCR replicated across three thermocyclers Biological replicates from same individual/timepoint Technical replicates with hot-start vs standard Taq Replicates tested across different technicians/shifts

Sensitivity Threshold * Select sensitivity level 0.5% - Ultra-sensitive for trace contamination 1% - Standard forensic threshold 2% - Balanced sensitivity/specificity 5% - Conservative industrial standard 10% - High-abundance artifact detection Variable per locus based on stutter ratios Dynamic threshold based on background noise Absolute read count minimum (≥10 reads) Signal-to-noise ratio cutoff (≥3:1) Custom threshold defined in additional parameters

Quality Control Metrics *

Reference Database * Select reference dataset CODIS US Population Database 1000 Genomes Project STR data In-house validated population frequencies EMPOP mitochondrial database US Y-STR database No reference - contamination vs signal analysis Custom laboratory population data NIST Standard Reference Materials International STR Sequence Repeat Database Regional/ethnic population substructure

Contamination Pattern Analysis * Select analytical approach Allele-specific contamination ratios Stutter peak pattern deviation Off-ladder artifact analysis Peak height imbalance assessment Statistical mixture analysis Reproducibility across replicates Quantitative contamination percentage Genotype concordance degradation Allele dropout/insertion patterns Comprehensive artifact profiling

Reporting Compliance Standards * Choose compliance level ISO 17025 forensic accreditation requirements SWGDAM guidelines compliance CLIA laboratory certification standards FDA bioanalytical method validation EPA Good Laboratory Practice Peer-review publication standards Internal laboratory SOP requirements Court-admissible documentation 21 CFR Part 11 electronic records Research grade documentation acceptable

Additional Context Parameters