Stepwise Threshold Clustering: A New Method for Genotyping MHC Loci Using Next-Generation Sequencing Technology
Figure 2
MDS plot of sequences in sample library X.
Small black dots indicate the 101unique sequences present in the sample library. Sequences have been plotted on the first two MDS axes generated using the same similarity matrix used during clustering, such that more similar sequences are closer together. The color of the larger circles indicates the final status of each sequence, whereas the size of each circle is proportional to the number of reads in the sample library that match that sequence (see Table S3 for list of sequences and their respective read numbers). Sequences indicated in red were combined with other more frequent sequences during phase 2. Sequences indicated in blue were deemed to be artifactual sequences. Allele #1238 (yellow) was not considered a good cluster in phase 3 (too small) but was considered a true allele after cross-checking in phase 4. The green circles indicate sequences corresponding to the other 6 true alleles. The dotted lines indicate the seven clusters (4 good, 1 ambiguous, 2 small) after the 97% similarity threshold had been reached in phase 3.