Could someone tell me what is a "plex" in sequencing?

[mandova]

I hear "multiplex" often, as in multitemplate PCR, multiplex PCR. What exactly is a plex?

[henry.wood]

It isn't really a biological term, it's an english language thing. It shows that something has more than one part. So something that is duplex has two parts, while something that is multiplex has many parts. Multiplex PCR is several pairs of primers in one tube to amplify several different products from the same starting DNA.

[mandova]

It isn't really a biological term, it's an english language thing. It shows that something has more than one part. So something that is duplex has two parts, while something that is multiplex has many parts. Multiplex PCR is several pairs of primers in one tube to amplify several different products from the same starting DNA.

THx!! So what is the consequence of using multiplex PCR instead of multitemplate PCR (if there's a technology that does) when a sequencing library is amplified...meaning, the implication of "multiplexing" in sequencing? Increased parallelism?

[gringer]

I think in sequencing multiplexing refers to doing an analysis of multiple samples at the same time.

[Simon Anders]

Multiplexing means that you sequence several samples in one flow-cell lane. To this end, you label each sample with a "barcode" (or "multiplex tag") by ligating adapters which contain the barcode in addition to the Illumina sequencing primers, so that the barcode will end up getting sequenced as if it were part of your fragment. Later, in analysis, you trim of the barcode and sort your reads according to it.

With HiSeq machine producing more tens of millions of reads, using a full lane for only one sample is often overkill, and multiplexing saves cost.

[mandova]

Multiplexing means that you sequence several samples in one flow-cell lane. To this end, you label each sample with a "barcode" (or "multiplex tag") by ligating adapters which contain the barcode in addition to the Illumina sequencing primers, so that the barcode will end up getting sequenced as if it were part of your fragment. Later, in analysis, you trim of the barcode and sort your reads according to it.

With HiSeq machine producing more tens of millions of reads, using a full lane for only one sample is often overkill, and multiplexing saves cost.

Thx all! And you happened to have answered my previous asked question which was not answered then...If I download a dataset from genebank, say Illumina reads, how do I know if the reads are single sample or barcoded multisample, just looking at the converted .sam file?

[krobison]

THx!! So what is the consequence of using multiplex PCR instead of multitemplate PCR (if there's a technology that does) when a sequencing library is amplified...meaning, the implication of "multiplexing" in sequencing? Increased parallelism?

Multiplex PCR is challenging because all of the possible primer interactions as well as differential amplification by the primers. By multi-template PCR I assume you mean amplifying many templates with a common set of primers, which is much easier to tune.