Sample type
FFPE
1
Biopsies
Fresh Frozen Biopsies
Skin Swabs
Serum
Negative water control
Pre-amplification treatment after WGA
E-Gel
-
E-gel
-
E-gel
UC
2
-
-
-
UC
2
UC
2
-
Sequencing platform
GS FLX
GS FLX
GS FLX
GS FLX
GS FLX
GS FLX
GS FLX
Ion PGM 300bp kit
Ion PGM 400bp kit
GS Junior
GS Junior
GS FLX
Human
63.9
37.3
95.5
99.8
42.6
2.1
69.1
77.3
76.3
23.6
37.3
2.8
Bacteria
14.6
21.3
3.1
0.1
36.8
61.1
24.2
18.3
18.3
36.8
26.3
52.2
Virus
0.0
0.2
0.0
0.0
0.1
0.1
0.3
0.4
0.3
0.7
0.8
0.0
Other
11.7
10.2
0.5
0.0
17.1
31.5
2.2
1.3
1.0
33.1
20.5
15.5
Unknown
9.8
30.9
0.9
0.0
3.5
6.1
4.2
2.7
4.1
5.9
15.1
29.5
1
Formalin Fixed Paraffin Embedded.
2
Ultracentrifugation.
Table 1:
Typical taxonomic assignmentof NGS reads (percent). Summary of results in previous studies using different types of biospecimens, pretreatments and NGS platforms [10,11].
