Sunday, January 29, 2012

Does Table Number 4 lie?

UPDATE: The questions that arise from table 4 can be found here.

At the end of this post is the table 4 from the addendum to Lombardi et al. 2009 (submitted in February 2010).

In this table we find:
  • Only 93 of the 101 patients are reported (WTF?)
  • 73/93 (78%) are positive by cDNA nested PCR
  • 17/93 (18%) are positive by DNA nested PCR
  • 34/45 (76%) are positive by LNCaP co-culture with PMCs 
  • 35/46 (76%) are positive by Antibody in plasma
  • 48/51 (94%) (!) are positive by LNCaP culture with plasma
Please note that PCR positive rate went up from 68/101 in Lombardi et al 2009 to 73/93 in the addendum.

When looking only at the 20 PCR negative patient samples, we find that:
This is simply unbelievable sloppy work (only 93 patient samples reported, reports at odds with information given in talks). Why weren't they called out for this? This is a bad joke.


Here is the table, the rows are:
  • Patient ID
  • cDNA nested PCR
  • DNA nested PCR
  • LNCaP co-culture with PMCs 
  • Antibody in plasma
  • LNCaP culture with plasma
(With "nt" = not tested)

1103 + + + + +
1104 + + + + +
1105 + - + + +
1106 + + + + +
1107 + - - nt nt
1108 + - - - -
1109 + - nt nt nt
1110 + - + + +
1111 + + + - +
1112 + - nt nt nt
1113 + - + nt nt
1114 + - nt nt +
1115 + - + + +
1116 - - nt nt +
1117 - - nt nt nt
1118 + - + + +
1119 + - nt nt nt
1120 - - nt nt nt
1121 + - nt nt nt
1124 + - - - -
1125 + - + + +
1126 + - nt nt nt
1127 + - nt nt nt
1128 + - nt nt nt
1129 + - nt - nt
1130 + - nt nt nt
1131 + - nt nt nt
1132 + + + nt nt
1133 + + nt nt nt
1134 - - nt nt nt
1135 + + nt nt nt
1136 + + - + +
1137 + + - + +
1265 + - + + +
1138 + - nt nt nt
1335 + - nt + +
1139 - - - - -
1140 + - nt - +
1141 + - + + +
1142 - - nt nt +
1206 + - nt - +
1144 + - nt nt nt
1145 - - nt nt nt
1148 - - nt nt nt
1149 + - nt nt nt
1150 + + + + +
1151 + - nt nt nt
1230 + - + nt nt
1237 + - + nt nt
1154 - - nt nt nt
1155 - - nt nt nt
1156 - - nt nt +
1157 + + nt nt nt
1158 + - - + +
1159 + - nt nt nt
1231 + - + nt nt
1161 + - - + +
1220 + - + nt nt
1221 + - + nt +
1164 - - nt nt nt
1165 + - + + +
1166 + - - + +
1167 - - nt nt nt
1168 + - nt nt nt
1169 + - + + +
1170 - - nt nt nt
1235 - - + nt nt
1281 + - + + +
1172 + + + + +
1282 + - - - +
1173 + + + + +
1174 + - nt nt nt
1175 - - nt nt nt
1176 - - nt nt nt
1177 + - + + +
1178 + - + + +
1179 + - nt - +
1180 - - nt + +
1181 + - nt nt nt
1182 - - nt + +
1183 + - - - +
1236 + - + nt nt
1224 + - nt nt +
1186 + + + + +
1187 - - nt + +
1188 + - + + +
1189 + + + + +
1190 + - + + +
1191 + - + + +
1192 + + nt + +
1193 + + nt + +
1194 + - nt - +
1238 + - + + +

Please notice the "odd" numbers (like 1206 or 1238), and the two "missing" patient numbers (1122 and 1123).

Focusing only on the PCR negative, first we have 8 patients tested by other methods (7 positive by other methods, 1 negative by all methods):
1116 - - nt nt +
1142 - - nt nt +
1156 - - nt nt +
1180 - - nt + +
1182 - - nt + +
1187 - - nt + +
1139 - - - - -
1235 - - + nt nt

And twelve patients were PCR negative but not tested (WTF?):
1117 - - nt nt nt
1120 - - nt nt nt
1134 - - nt nt nt
1145 - - nt nt nt
1148 - - nt nt nt
1154 - - nt nt nt
1155 - - nt nt nt
1164 - - nt nt nt
1167 - - nt nt nt
1170 - - nt nt nt
1175 - - nt nt nt
1176 - - nt nt nt

(Sorry if the formatting of the table is garbled up, I can't post it any better; You can look up the table in the PDF)

Update: I uploaded the spreadsheet here.

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