{"id":11996,"date":"2019-02-13T17:19:50","date_gmt":"2019-02-13T17:19:50","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=11996"},"modified":"2019-02-13T17:57:18","modified_gmt":"2019-02-13T17:57:18","slug":"simplified-pgt-workflow-on-a-single-embryo-biopsy","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/simplified-pgt-workflow-on-a-single-embryo-biopsy\/","title":{"rendered":"Simplified PGT Workflow on a Single Embryo Biopsy"},"content":{"rendered":"

Bioarray<\/a>\u00a0is an innovative diagnostic and research laboratory located in Alicante, Spain.<\/p>\n

Luis Alcaraz, PhD<\/p><\/div>\n

There, scientists specialize in human genetic analysis using a variety of molecular techniques such as\u00a0microarray<\/a>\u00a0and\u00a0next- generation sequencing<\/a>\u00a0(NGS) technologies, including gene panels as well as whole-exome sequencing. Bioarray offers a broad menu of testing options, from clinical\u00a0and reproductive genetics to research services, with expertise in\u00a0preimplantation genetic screening(PGS) as well as bioinformatics.<\/p>\n

Luis Alcaraz, PhD, is the scientific and laboratory director of Bioarray as well as its cofounder. He is a researcher in the field of proteomics and genomics, with comprehensive experience in bioinformatics using high-throughput techniques.<\/p>\n

Thermo\u00a0Fisher Scienti\ufb01c:\u00a0<\/strong>You\u00a0recently\u00a0made\u00a0some significant\u00a0changes\u00a0to the\u00a0platform\u00a0you use for\u00a0preimplantation genetic screening (PGS).Can\u00a0you\u00a0please\u00a0tell us what those\u00a0changes\u00a0are,\u00a0and why you\u00a0made them?<\/p>\n

Alcaraz:<\/strong> For PGT-A, we found the scalability of the\u00a0Ion ReproSeq\u2122\u00a0PGS workflow<\/a>\u00a0to be advantageous to our laboratory, accommodating various sample throughputs, low or high. Therefore, as our laboratory sample throughput increases, our Ion Torrent platform grows with us; we simply purchase a different chip to accommodate higher sample throughput. The time-to-results and total hands-on time are also incredibly important to our laboratory; with the Ion\u00a0ReproSeq kits, we can go from cells to data in 10\u201313 hours with only 2\u20133 hours of hands-on time, depending on sample throughput.<\/p>\n

PGT-M is particularly challenging because traditionally it\u2019s been very expensive, it\u2019s difficult to design STR primers for specific disorders, and it\u2019s not easy to combine with PGT-A. PGT-M requires a lot of expertise in primer design for interrogating specific STRs. The primers must be tested for every couple undergoing fertility treatment, and sometimes redesign of primers is needed\u2014making the process quite lengthy, even up to several months long.<\/p>\n

This is important because couples become stressed and do not want to wait that long. This entire process is\u00a0expensive. Additionally, it\u2019s neither easy nor cost-effective to combine PGT-A and PGT-M, because the workflows are completely different. So quite often, couples undergoing PGT-M can\u2019t benefit from PGT-A for economic reasons.<\/p>\n

Lastly, allele dropouts are a major concern for PGT-M, due to whole-genome amplification (WGA). For this reason, analysis of the single mutation is not enough; we need to also perform linkage analysis with several polymorphisms around the mutation.<\/p>\n

We have been able to overcome these challenges now with\u00a0Ion AmpliSeq\u2122\u00a0technology<\/a>\u00a0and Ion ReproSeq\u2122\u00a0chemistry, which work beautifully together. We can use a single biopsy for both applications, more cost-effectively. We have successfully integrated our simplified workflows for PGT-A and PGT-M in our lab with Thermo Fisher\u2019s solutions.<\/p>\n

Thermo Fisher:<\/strong> Do you have an example you can share with us to illustrate exactly how this works?<\/p>\n

Alcaraz:<\/strong> Here at Bioarray, we have had tremendous success with our custom-designed kits for PGT-M based on the trusted Ion AmpliSeq technology. It is recognized globally as the gold-standard, amplicon-based enrichment method for targeted NGS. We build kits of custom NGS panels to include a 2 Mb flanking sequence on either\u00a0side of the mutation locus region for linkage analysis. The PGT-M kits are designed to be used simultaneously with a single embryo biopsy required for the Ion ReproSeq\u00a0workflow for PGT-A, and require only 3 \u00b5L of WGA product to start. Our unique single-nucleotide polymorphism (SNP) phasing technology and bioinformatics solution enables fast analysis of specific mutations and generates a report post\u2013variant calling.<\/p>\n

One common case example we see here in Europe is CFTR: I will outline the workflow for you. First, we need to perform the amplification and library preparation of the embryos. After checking the amplification, we need to take a small aliquot (about 3 \u00b5L) of the library and we use a Bioarray PGD-Seq Kit based on the Ion AmpliSeq technology to construct the library for PGT-M. Then we combine the Ion ReproSeq and PGD-Seq libraries to be loaded onto one single Ion chip for sequencing. At the same time, we need to analyze parental and relatives\u2019\u00a0samples to perform the linkage analysis. After sequencing, we do the analysis of both PGT-A with Ion ReproSeq and PGT-M with PGD-Seq software. Finally, we combine both results to detect not only those embryos that are healthy, but also those that are euploid, increasing the effectiveness of the cycle.<\/p>\n

Our Bioarray PGD-Seq Kits are available for virtually all single-gene disorders, including cystic fibrosis, spinal muscular atrophy, beta-thalassemia, polycystic kidney disease, fragile X syndrome, and others.<\/p>\n

Thermo Fisher:<\/strong> What advice do you have for other laboratories who may be running aCGH or thinking of consolidating PGT-A and PGT-M workflows?<\/p>\n

Alcaraz<\/strong>: For aneuploidy testing, aCGH is an obsolete technique. Now we know how important it is to correctly identify mosaic embryos, and thanks to the higher accuracy and sensitivity of NGS, we can categorize the embryo as normal, abnormal, or mosaic. Moreover, we can use the last category as the last chance for many couples when there are no more normal embryos.<\/p>\n

Another important point is around PGT-M. Nowadays, thanks to the wide use of carrier screening panels, many couples know that they are at risk of having a child affected by a recessive disease. Now they have the opportunity to detect which embryos are not affected by the disease.<\/p>\n

Thanks to NGS, integrating the PGT-M workflow with PGT-A has several advantages, including no investment needed for additional equipment. Classically, PGT-M requires a capillary sequencer, but now with the Ion\u00a0AmpliSeq technology, it is possible to perform testing with the same equipment you already have for PGT-A. Both PGT-M and PGT-A can be run on the Ion\u00a0GeneStudio\u2122<\/a>\u00a0S5 System<\/a>. Another advantage is less sample handling is needed, thereby reducing the possibility of error.\u00a0Combining\u00a0both protocols is more cost-effective, allowing more\u00a0couples\u00a0to\u00a0benefitfrom\u00a0PGT-A\u00a0and\u00a0PGT-M.Lastly, we have the advantage of robust\u00a0bioinformatic analysis\u00a0for both\u00a0PGT-Aand\u00a0PGT-M.\u00a0Our simplified\u00a0PGT-A\u00a0andPGT-M\u00a0workflow\u00a0on a\u00a0single\u00a0embryo\u00a0biopsy has\u00a0transformed\u00a0the testing we\u00a0can\u00a0offer.<\/p>\n

 <\/p>\n

<\/p>\n

<\/p>\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

Bioarray\u00a0is an innovative diagnostic and research laboratory located in Alicante, Spain. There, scientists specialize in human genetic analysis using a variety of molecular techniques such as\u00a0microarray\u00a0and\u00a0next- generation sequencing\u00a0(NGS) technologies, including gene panels as well as whole-exome sequencing. Bioarray offers a broad menu of testing options, from clinical\u00a0and reproductive genetics to research services, with expertise in\u00a0preimplantation<\/p>\n","protected":false},"author":120,"featured_media":11994,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[182],"tags":[],"division":[],"class_list":{"0":"post-11996","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-reproductive-genomics","8":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nSimplified PGT Workflow on a Single Embryo Biopsy - Behind the Bench<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/simplified-pgt-workflow-on-a-single-embryo-biopsy\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Simplified PGT Workflow on a Single Embryo Biopsy\" \/>\n<meta property=\"og:description\" content=\"Bioarray\u00a0is an innovative diagnostic and research laboratory located in Alicante, Spain. 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Rather than changing the underlying DNA sequence, epigenetic changes influence how genes are expressed, including when they are turned on, turned off, or regulated in response to biological and environmental signals. 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Every downstream application, from PCR to next-generation sequencing (NGS), depends on starting with nucleic acids that are accurately quantified and free from contaminants that could compromise results. Establishing a consistent quality control workflow helps laboratories improve reproducibility\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"A pipette drops a liquid into a petri dish with a dna sequence background, science concept. 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A standardized workflow combining reliable extraction, concentration and purity assessment, application-appropriate quantification, and consistent laboratory practices can help identify sample issues early, improve reproducibility,\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Close-up shot of a dna sequence on a screen, a digital representation of genetic code, used for analysis.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19997,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/ai-laboratory-automation-qpcr\/","url_meta":{"origin":11996,"position":5},"title":"AI and Laboratory Automation: The experimental context behind qPCR data","author":"Behind The Bench Staff","date":"September 11, 2026","format":false,"excerpt":"AI is changing how researchers analyze biological data, while automation is changing how that data is performed at scale. 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