Forensic SNP Genotyping using Nanopore MinION Sequencing

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1 Forensic SNP Genotyping using Nanopore MinION Sequencing AUTHORS Senne Cornelis 1, Yannick Gansemans 1, Lieselot Deleye 1, Dieter Deforce 1,#,Filip Van Nieuwerburgh 1,#,* 1 Laboratory of Pharmaceutical Biotechnology, Ghent University # Contributed equally * Corresponding author at: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Gent, Belgium. Supplementary Information

2 Oxford Nanopore Illumina rs C T C T rs A G A G rs G G G G rs A G A G rs T T T T rs G G G G rs A A A A rs C T C T rs A A A A rs A T A T rs A A A A rs G G G G rs T T T T rs A G A G rs G G G G rs A A A A rs C C C C rs A G A G rs G G G G rs C C C C rs C C C C rs G G G G rs G G G G rs C C C C rs C T C T rs G G G G rs A A A A rs A A A A rs C T C T rs T T T T rs C C C C rs A T A T rs * A C C C rs T T T T rs A A A A rs T T T T rs C T C T rs A G A G rs A A A A rs G G G G rs C T C T rs A A A A rs T T T T rs C C C C rs A C A C rs T T T T rs A G A G rs A G A G rs C C C C rs G G G G rs T T T T rs C T C T Supplementary Table 1: Sample 9947A SNP profiles generated with Oxford Nanopore and Illumina sequencing. Discordant loci are indicated by a red asterisk.

3 Forward primer sequence Reverse primer sequence rs GTGTGGACTGGGCTGATGT TTCTCACTAGTGTCCCTGCTCTG rs GCAGGCTCCATTTTTATACCACT GAATATCTATGAGCAGGCAGTTAGC rs AGCTGATGCAGACCACTTCAC GGATAGCTGATAAGAAACATGACCA rs CCTATTTGTATGTATCTATTGTCTATGAACG GTCATTGTTGACACTTCACCTTCTA rs CTTTAGAAAGGCATATCGTATTAACTGTG AACACAGAAAGAGGTTCATATGTTGG rs CATAACGTGGATTTGTCAGCA GGAATAAACTGAAGGCTAAAGAAAAG rs GCCCTTTAGGGTCGGTTC GTAAGAGATGACTGAGGTCAACGAG rs ATCAAGTGCTTTCTGTTGACATTTG GGCTACTCCCTCATAATGTAATGC rs AAGTGATGGAGTTAGGAAAAGAACC AAGACATTAGGTGGATTCATAGCTG rs GGAGAAAACCGGAGAGCTG GAGTGTCACCGAATTCAACG rs CTGGGTGCAAACTAGCTGAATATC CTGGAATGTACTAGGCAAGAAACTAA rs GAGCATTCTCTTCTGTTAAAATTGC TGAGTACATTATTCAACTGTTTTGGAG rs GTCCTTGTCAATCTTTCTACCAGAG GGATTTTCACAACAACACTTGC rs AGGGAAATACACCCTGAGCTG AGCTGTCCATCATCAGTAAGACAC rs TGCATCCCAGCCTCCACT ATTGTACCTTGCCACTTTGTGTG rs CATTAATATGACCAAGGCTCCTCT ACATTTCCCTCTTGCGGTTAC rs GTATAACAGTTTGCTAAGTAAGGTGAGTG AGATAGGTTCGAGTTTTGGCTTTA rs CTATTCTCTCTTTTGGGTGCTAGG CAAACTGTTTATTGTGAGGCCTGT rs CACAGCATCTTTTAACTCTTTTATTATCC GTAAGGACTTATAGTGAGTAAAGGACAGG rs CTTATCTTTCCCACATTATGGTCCT AAGATATAATCACTGCTTTCAAGTATGC rs GGAAGTACACATCTGTTGACAGTAATGA GGGTAAAGAAATATTCAGCACATCC rs AGCTTTCAGCCCCAGGTC CGGCTCAGGAATGTCAGG rs TGAATTTTGTCTCTGTTATATTAGTCACC TGTAATTGAAATTTGTAGGCAATAGAC rs GGCTAAACTATTGCCGGAGA TTCCCTAGAACCACAATTATCTGTC rs GCATTCAAATCCCAAGTGCT GCAGGAGTTGGAGTCAATCAG rs ACGAAGGAGAAACACCTGAACT TGGAGTACTTAATAAGACGCTGCAT rs AGCATCTTGGCAGCATCC AGCAAGATCTTTGCCAGTGAGT rs CCAAACTGGGTGTTAGGGAGAC TCATTATCTCGTCATACTTCCCTGT rs CCATGTGTTCTAATAAAAAGGATTGC TGGGAAGTGAGCAAAAGTAAATACA rs GTGTTTCTTTTTCTCTTACCGGAAC GTGAATGAAATCATGAGATTGCTG rs AACCTCCTTTGGAAACACTGAC CAACATTCCATTATCCAGGAGAC rs CATTGAAGTCCTAACCCCTAGTACG GGATGAGGCCCACCCATA rs TCAGAGACTATGGATGGTATTTAGGTC CATGGAACGTTGGAACTCTTG rs ACTATCAGTCTCTGCCCTTATTCTG CACATGTGCATGCTTTTGG rs GCCTCACCACCAGAAATCAG GACATCAGAAACTCCCATGAAACT rs CCATGATTTTCTTGTGGTGAGA CACATGTGCTTAGGCCACAAC rs GGAGTTCCTGATAACGATTCTGAAG ACAGAAAAGAAGCCCAGTTGGA rs GGCTTCTCTTTCCCTTATGTATCTC CAGGTTGCGATAGAAAACAGTGAAT rs TCTGGAATGCCAGTTCTTTTGT CAGAACGCCTATGAAAACCAGT rs ACATGTGAGGCCATCTCCAC CCTTACTGTGATGTAGGCACTGTTC rs CACTTCTATAGACATAGGACACACCAT ATCTAGGCTCTGAATCAGGATGAG rs AGAGGGCAGTGAGGCTTTTAAGTAG TGCTAGAATCCAGACTTAACTACCAG rs AGCAGCAGAGCCTGGATG AGACCAGTCACCTCTTTTGCACT rs AGATCTCCACTTCCTCTTGGTTG CTCCCAAATTTACATTGCCACT rs AGACTCTCTGTGTGTGGCTTTG GAGGGGGCATCTGTTGAG rs GTACCTGGAGGTGATTTCTGTGAG GTTATGGAGGATTGGTAAGAACCAG rs GGTTTGTGTGTGAGTGTTTCAGAT CCTTATGCCTCCCCTGAAC rs TTCACTTTGCTACACCTCCATAGTA TGCTACGTAAGAGGTCATTGCTATC rs TTTTCAGAGGTGGTATTTCTAGCTG GCTATGACACTCCTTAGAACTATGCAA rs GTGGATGATATGGTTTCTCAAGG TTCAACAAACGTGTGATGCTCT rs ACAGCTGATGCCTCCCTGA GAGGATGAAGGTTAGAGCCAGAC rs TCCTGGAGATCAATATTTAGCCTTA GGGTGACCAGTAGTTCTATGAGC Supplementary Table 2: Forward and Reverse PCR primer sequences for the 52 SNPforID loci

4 Supplementary Figure 1: IGV screenshots of the mapped reads at locus rs (top) and rs (bottom)

5 Supplementary Figure 2: IGV screenshots of the mapped reads at locus rs (top), rs (middle) and rs (bottom).

6 Relatieve frequency Subread count Supplementary Figure 3: Number of extracted subreads per SNP locus (grey) and number of mapped subreads against the SNP reference sequence per SNP locus (black) using the BWA ONT2D setting. 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% Supplementary Figure 4: Relative frequency of mapped subreads using the BWA ONT2D setting containing one of the two possible SNP alleles (grey and black). Red bars show the proportion of reads containing an unexpected base at the SNP position. The allelic imbalance cut-offs are indicated by dashed lines. Loci discordant with the Illumina reference are indicated with an asterisk.

7 Relatieve frequency 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% Supplementary Figure 5: Relative frequency of mapped subreads using 1 percent of the available data containing one of the two possible SNP alleles (grey and black). Red bars show the proportion of reads containing an unexpected base at the SNP position. The allelic imbalance cut-offs are indicated by dashed lines. Loci discordant with the Illumina reference are indicated with an asterisk.