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Alignment percentages of both datasets are reported in Table 2.

Previous studies report alignment percentages from as low as 70% up to 94% [ 24, 27, 50– 50].

Only results with score ratios over 0.2 and alignment percentages above 60% were kept for further studies.

Longer tag sequences, higher alignment percentages and more stringent gap and mismatch scores will result in more accurate tag sequence identification.

Trimming 4 bp and 9 bp from 5′ end resulted in a larger improvement in alignment percentages (84 and 89%, respectively), which is likely the result of removing low quality information from the reads.

Among the 260 hits, 2 UTs had matches with I. multifiliis ESTs with low E values (10-7 and 10-9 respectively) and another 27 hits had an alignment percentages of more than 50%.

A typical alignment percentage defined as number of uniquely aligned reads over total pass filtered reads was around 55-65%.

The alignment percentage per patient using ΔSUV and Δ percentage is detailed in Table 2.

RECIST tumor response was not related to the thoracic alignment percentage.

If there were any large discrepancies (i.e., <80% alignment using ΔSUV), we further investigated the reason for this low alignment percentage.

Table 1 Alignment percentage per patient between elastix and baseline image of intra- and extra-thoracic measurable lesions Pts       Thoracic Extra-thoracic   Age Sex RECIST N % ΔSUV %Δ perc.