Tag: laboratory test limitations

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects

Abstract:

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified.

We used metagenomics to analyse the RNA from plasma samples from 25 individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25).

We found that the majority of sequencing reads were removed during host subtraction, thus there was very low microbial RNA content in the plasma. The effects of sample batching and contamination during sample processing proved to outweigh the effects of study group on microbial RNA content, as the few differences in bacterial or viral RNA abundance we did observe between study groups were most likely caused by contamination and batch effects.

Our results highlight the importance of including negative controls in all metagenomic analyses, since there was considerable overlap between bacterial content identified in study samples and control samples. For example, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodes were found in both study samples and plasma-free negative controls. Many of the taxonomic groups we saw in our plasma-free negative control samples have previously been associated with diseases, including ME/CFS, demonstrating how incorrect conclusions may arise if controls are not used and batch effects not accounted for.

 

Source: Miller RR, Uyaguari-Diaz M, McCabe MN, Montoya V, Gardy JL, Parker S, Steiner T, Hsiao W, Nesbitt MJ, Tang P, Patrick DM; CCD Study Group. Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects. PLoS One. 2016 Nov 2;11(11):e0165691. doi: 10.1371/journal.pone.0165691. ECollection 2016. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5091812/ (Full article)

 

Cognitive performance and complaints of cognitive impairment in chronic fatigue syndrome (CFS)

Abstract:

Patients with chronic fatigue syndrome (CFS) complain that they have difficulties with concentration and memory but studies to date have not found consistent objective evidence of performance deficits.

Two groups of CFS patients, depressed and non-depressed, and healthy controls, were asked about concentration problems in general and specifically when reading. CFS subjects were more likely than controls to report that they had concentration problems when reading, that they needed to re-read text and that they failed to take in what they were reading.

Subjects then performed a task in which their reading behaviour and text recall was measured. While all CFS subjects complained of general cognitive failures and of difficulties with reading, only depressed CFS subjects recalled significantly less of the text than controls. Severity of complaints about reading problems was not related to amount of text recalled, but was related to severity of depressed mood. However, subjects were able to evaluate accurately their ability to remember the text immediately after reading it and before being tested for recall.

Additionally, subjects performed a paired-associate learning task on which no significant differences between the subject groups was found. It is concluded that deficits in cognitive functioning in CFS patients are more likely to be found on naturalistic than on laboratory tasks.

 

Source: Wearden A, Appleby L. Cognitive performance and complaints of cognitive impairment in chronic fatigue syndrome (CFS). Psychol Med. 1997 Jan;27(1):81-90. http://www.ncbi.nlm.nih.gov/pubmed/9122311