TraceHaplotyper: Using Direct Sequencing to Determine the Phase of an Indel Followed by Biallelic SNPs

Seroussi, Yanir; Seroussi, Eyal

doi:10.2144/000112552

Cited by 9 publications

(5 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, a method that would enable the separation of alleles or gene copies in direct sequencing is preferable to subcloning. Seroussi & Seroussi (2007) and Dmitriev & Rakitov (2008) have developed computer methods that deconvolute two alleles from polymorphic traces including indels. When indels are not too long and the trace data are of high quality, these tools have high accuracy, but they may still fail under some circumstances.…”

Section: Introductionmentioning

confidence: 99%

Use of allele‐specific sequencing primers is an efficient alternative to PCR subcloning of low‐copy nuclear genes

Scheen

Pfeil

Petri

et al. 2011

Molecular Ecology Resources

View full text Add to dashboard Cite

Direct Sanger sequencing of polymerase chain reaction (PCR)-amplified nuclear genes leads to polymorphic sequences when allelic variation is present. To overcome this problem, most researchers subclone the PCR products to separate alleles. An alternative is to directly sequence the separate alleles using allele-specific primers. We tested two methods to enhance the specificity of allele-specific primers for use in direct sequencing: using short primers and amplification refractory mutation system (ARMS) technique. By shortening the allele-specific primer to 15-13 nucleotides, the single mismatch in the ultimate base of the primer is enough to hinder the amplification of the nontarget allele in direct sequencing and recover only the targeted allele at high accuracy. The deliberate addition of a second mismatch, as implemented in the ARMS technique, was less successful and seems better suited for allele-specific amplification in regular PCR rather than in direct sequencing.

show abstract

Section: Introductionmentioning

confidence: 99%

Use of allele‐specific sequencing primers is an efficient alternative to PCR subcloning of low‐copy nuclear genes

Scheen

Pfeil

Petri

et al. 2011

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…Finally, a number of programmes have been developed to deconvolute sequences downstream from heterozygous indels; these include: C hampuru (Flot 2007), I ndelligent (Dmitriev & Rakitov 2008) and T race H aplotyper (Seroussi & Seroussi 2007). While potentially useful for HapSTR loci, the accuracy of these programmes depends on all double peaks in a given sequence being accurately assigned IUPAC degeneracy codes.…”

Section: Resultsmentioning

confidence: 99%

Genotyping HapSTR loci: phase determination from direct sequencing of PCR products

Sorenson

DaCosta

2011

Molecular Ecology Resources

View full text Add to dashboard Cite

HapSTRs combine information from a microsatellite (or simple tandem repeat, STR) with one or more single nucleotide polymorphisms in the DNA sequence immediately flanking the STR. These loci may offer increased power for the estimation of demographic parameters, but also present some challenges for data collection and analysis. We describe a process for inferring HapSTR alleles, including the flanking haplotypes, STR alleles and their phase relative to each other, directly from DNA sequence electropherograms of PCR products from heterozygous individuals. Our approach eliminates the need for more costly and time-consuming processes, such as cloning or acrylamide gel electrophoresis to separate alleles prior to sequencing.

show abstract

“…37 Alternative adaptations were observed in the affected hip joint during early stance phase, where increased work was thought to propel the body forward from the rear. 44,45 In terms of prosthetic fitting, devices used by subjects with TMT and Lisfranc amputations (toe fillers, slipper sockets, and ankle-foot orthosis), which were designed to allow relatively unrestricted ankle motion, did not improve ankle function compared to the clamshell patellar tendon bearing (PTB) prosthesis used by subjects with Chopart amputations in whom ankle motion was eliminated.…”

Section: Discussionmentioning

confidence: 99%

Preservation of Residual Foot Length in Partial Foot Amputation: A Biomechanical Analysis

Dillon¹,

Barker²

2006

Foot Ankle Int.

View full text Add to dashboard Cite

The primary reason for a partial foot amputation is to preserve the normal function of the foot and ankle complex associated with push-off. As such, surgery should strive to preserve the metatarsal heads to allow amputees to use the ankle's contribution to walking. Given that amputation proximal to the metatarsal heads compromised the normal propulsive function of the foot and ankle, surgery should not strive to preserve residual foot length to maintain function but should instead aim to achieve good distal tissue coverage and healing, particularly given that the hip joint(s), not the ankle, become the primary source of power for walking.

show abstract

TraceHaplotyper: Using Direct Sequencing to Determine the Phase of an Indel Followed by Biallelic SNPs

Cited by 9 publications

References 13 publications

Use of allele‐specific sequencing primers is an efficient alternative to PCR subcloning of low‐copy nuclear genes

Use of allele‐specific sequencing primers is an efficient alternative to PCR subcloning of low‐copy nuclear genes

Genotyping HapSTR loci: phase determination from direct sequencing of PCR products

Preservation of Residual Foot Length in Partial Foot Amputation: A Biomechanical Analysis

Contact Info

Product

Resources

About