tuberculosis DNA in all the pleural TB samples, thus demonstrating that the DNA extraction method could affect the performance of real-time PCR. Because of extremely high sensitivity of PCR, the carry-over contamination of amplicon, previous infection

or asymptomatic EPTB infection at another site could result into false positivity (Honore-Bouakline et al., 2003; Chakravorty et al., 2005; Sun et al., 2011). The false positivity of PCR reports in the absence check details of clinical findings poses serious challenges these days in diagnosing EPTB cases (Thangappah et al., 2011). The lack of proper gold standard remains the major hindrance for evaluating new diagnostics in EPTB-infected individuals (Sun et al., 2011; Vadwai et al., 2011). The true accuracy of PCR tests may actually be different than the reported one when using an imperfect gold/reference standard (Abbara & Davidson, 2011; Tortoli et al., 2012). Culture (on solid and liquid media) is the most widely used gold standard for validating PCR results in diagnosing EPTB specimens although it is suboptimal gold standard with varying sensitivities and leads to inaccurate PCR

results (Negi et al., 2005a; Hillemann et al., 2011; Sun et al., 2011). MLN0128 cell line The other gold/reference standards include BACTEC culture, histopathology and response to anti-tubercular therapy (ATT) and also the combination of these methods (Negi et al., 2005b; Kulkarni et al., 2006; Abdalla et al., 2009; Noussair et al., 2009). Chakravorty et al. (2005) as well as Vadwai et al. (2011) have used smear, culture, histology/cytology, clinical findings and response to ATT, all together as the gold/reference standard for validating

their PCR results in diagnosing EPTB specimens. There are several potential commercial kits Farnesyltransferase devised to diagnose TB such as Amplicor M. tuberculosis test (Roche Molecular Systems Branchburg, NJ), Gen-probe Amplified M. tuberculosis Direct Test (AMTD; Gen-Probe, CA), COBAS TaqMan M. tuberculosis (Roche Molecular Systems Branchburg) and LightCycler (Roche Molecular Diagnostics, Mannheim, Germany; Ritis et al., 2005; Causse et al., 2011; Parrish & Carroll, 2011) Among these, Amplicor M. tuberculosis test and AMTD based on 16S rRNA gene have been approved by the US Food and Drug Administration (FDA) for the diagnosis of PTB only (Brodie & Schluger, 2009), and none of these commercial tests have been approved by FDA for the diagnosis of EPTB (Parrish & Carroll, 2011). However, the utility of these commercial tests has been extensively explored in the diagnosis of EPTB (Honore-Bouakline et al., 2003; Causse et al., 2011). Moreover, the meta-analyses of PCR tests have suggested that the commercial tests yielded high specificities but variable sensitivities for the diagnosis of EPTB, while heterogeneous sensitivities and specificities were observed with in-house PCR tests (Pai et al., 2004; Daley et al., 2007).