pad hopping errors

geopiet Nov 13, 2020:

... .. 'pad-hopping' events where a single DNA-insert is copied and migrates to multiple adjacent wells on a patterned flow cell. - https://dspace.mit.edu/bitstream/handle/1721.1/104556/958632... - page 21

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Modyfikacja długości nici i sekwencji nukleotydów pozwoliła stwierdzić, że do procesów składających się na przenoszenie ładunku w DNA należą przeskakiwanie (ang. hopping) pomiędzy resztami G oraz tunelowanie przez parę zasad T:A [7,17], - http://rcin.org.pl/Content/34641/WA488_24083_P939_T56-z1-PB.... - pages 27 and 31

Frank Szmulowicz, Ph. D. Nov 13, 2020:

Pad hopping" refers to contamination of nearby nanowells which may lead to mixed clusters or at worst identical sequence clusters in physically close nanowells.
http://seqanswers.com/forums/showthread.php?t=70498

Optical duplication by pad hopping is specific to the arrayed flowcell
technologies. With insufficient DNA loading, a strand of DNA will “hop” from an already seeded well to a neighboring one causing identical clusters.
http://genomics.broadinstitute.org/data-sheets/POS_Enablingp...

Paweł Janiszewski (asker) Nov 13, 2020:

Znalezione "HiSeq X uses ordered flowcells (like HiSeq 3000/4000). There is a need to control insert size (between 350-450 bp, ideally) with ordered flowcells to avoid generation of optical duplicates due to pad hopping (DNA fragments contaminating multiple wells nearby during the ExAmp procedure)."

http://seqanswers.com/forums/archive/index.php/t-72379.html

Also, with single-molecule sequencing, there is little or no risk of “pad-hopping”, whereby a cluster grows across the interstitial space and creates a neighboring duplicate

https://www.freepatentsonline.com/y2019/0276886.html

Optical duplication by pad hopping is specific to the arrayed flowcell technologies. With insufficient DNA loading, a strand of DNA will “hop” from an already seeded well to a neighboring one causing identical clusters

http://genomics.broadinstitute.org/data-sheets/POS_Enablingp...