Genetic testing during IVF

Planning for a healthy baby now comes with a variety of genetic testing options at various points throughout the process. Prospective parents often encounter terms like NIPT, PGT-A, and Orchid’s PGT-WGS (Preimplantation Genetic Testing via Whole Genome Sequencing). Each test provides unique insights at different stages of the journey.

In this guide, we’ll compare Orchid’s whole-genome preimplantation genetic screening (PGT-WGS) with traditional preimplantation genetic testing for aneuploidy (PGT-A). We’ll also explore how embryo screening compares to prenatal options during pregnancy such as non-invasive prenatal testing (NIPT), chorionic villus sampling (CVS), and amniocentesis, to help you better understand their capabilities and limitations—so you can make an informed decision.

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Genetic Testing Available Before Pregnancy

For those undergoing in vitro fertilization (IVF), preimplantation genetic testing (PGT) allows embryos to be screened before they are implanted for pregnancy. There are different types of PGT designed to look for different genetic conditions, with the most common being PGT-A.

During IVF, embryos are biopsied, a process where a few cells are removed and analyzed based on the specific type of PGT ordered. However, it’s important to note that the cells being biopsied come from the part of the embryo that will develop into the placenta, not the baby. Because of this, every type of PGT, no matter what lab performs it, is considered a screening test, not a diagnostic test. To confirm results, diagnostic testing during pregnancy; such as chorionic villus sampling (CVS) or amniocentesis, is recommended. Learn more about the biopsy itself here.

Embryo Screening with PGT-A 

Preimplantation Genetic Testing for Aneuploidy (PGT-A) allows screening of embryos created through IVF before they are implanted for pregnancy for chromosomal abnormalities. PGT-A identifies euploid embryos (with a normal set of 46 chromosomes) to select for transfer (What you need to know about genetic tests available before and during pregnancy). PGT-A can also determine an embryo’s sex. However, a key limitation is that PGT-A only checks chromosome counts – it cannot detect if an embryo carries a mutation for a single-gene disease like cystic fibrosis, nor can it assess risk for complex disease like diabetes or heart disease. Since PGT-A is designed only to check for large scale imblances in the amount of genetic material, , this means an embryo deemed chromosomally normal by PGT-A could still have inherited a serious genetic condition or a predisposition to disease that would go unnoticed. Traditional PGT-M (targeted gene testing) can be added for known single-gene risks, but it must be designed on a case-by-case and is limited to diseases for which there is a known risk in the family based on previous genetic test results.

Embryo Screening with Orchid’s Whole-Genome Sequencing

Orchid’s Whole Genome Sequencing PGT (PGT-WGS) is an advanced preimplantation test that provides more information than any other PGT method. Like PGT-A, it begins with an IVF embryo biopsy, but instead of examining just a few genetic markers, Orchid sequences over 99% of the embryo’s DNA at high depth (What's in Orchid's Embryo Report?). This comprehensive approach means that Orchid’s test includes standard aneuploidy screening and goes far beyond it. Orchid can identify subtle chromosomal microdeletions or duplications that are linked to developmental disorders – even those too small for standard PGT-A to catch. More impressively, Orchid is the only embryo screening that conducts broad monogenic disease screening for hundreds of conditions caused by single-gene mutations (What's in Orchid's Embryo Report?). In total, Orchid’s whole-genome report can screen for over 1,200 genetic conditions linked to severe childhood disorders, inherited cancers, and other serious diseases, all in one test (What you need to know about genetic tests available before and during pregnancy).

Beyond single-gene defects, Orchid’s embryo report can optionally assess polygenic risk scores – the combined effect of many genes on common health conditions. This means parents receive insight into an embryo’s genetic predisposition to common, chronic ailments like heart disease, diabetes, or certain adult-onset cancers (What's in Orchid's Embryo Report?). Such complex disease risks are not examined by traditional prenatal tests. With Orchid, couples can choose an embryo not only free of known genetic disorders, but also one with lower risk for future illnesses. All of this information is provided before pregnancy, giving would-be parents knowledge that used to be available only after birth (if at all) (Startup Launches Test to Identify Defects Before IVF Pregnancy - Human Progress). Orchid’s service includes genetic counseling to help interpret this wealth of data and guide next steps, ensuring families feel supported in making the best decision for their future child. 

Learn more about the different types of PGT here. 

Genetic Testing Available During Pregnancy

The main difference between preimplantation genetic testing (PGT) and tests like NIPT, CVS, or amniocentesis is that the latter are performed during pregnancy, whereas PGT is conducted on embryos created via IVF before implantation. Like PGT, non-invasive prenatal testing (NIPT) is considered a screening test, meaning any abnormal results should be confirmed through diagnostic testing, such as amniocentesis.

NIPT (Non-Invasive Prenatal Testing) is a blood test performed early in pregnancy (around 9–10 weeks). It analyzes tiny fragments of fetal DNA in the mother’s blood to screen for a few major chromosomal abnormalities. NIPT is primarily used to detect conditions caused by an atypical number of chromosomes, such as trisomy 21 (Down syndrome) (What you need to know about genetic tests available before and during pregnancy). It can also reveal the baby’s sex and sometimes small chromosomal deletions or duplications. Importantly, NIPT is a screening tool and any high-risk NIPT finding is usually confirmed with a diagnostic test like amniocentesis later in pregnancy (What you need to know about genetic tests available before and during pregnancy). Like PGT, NIPT relies on cells from the placenta - so, while it is a valuable screening tool in pregnancy it is not the preferred method to confirm any results from embryo screening.

Amniocentesis is a diagnostic test done mid-pregnancy (around 16–20 weeks). A doctor uses a needle to withdraw a small sample of amniotic fluid, which contains fetal cells. This test can detect the same chromosomal conditions as NIPT, PGT-A and Orchid’s (PGT-WGS) but is used for confirmation. If there is a known risk or concern—such as a birth defect detected via ultrasound—amniocentesis can be used to test for certain single-gene disorders that may not be identifiable through PGT. While amniocentesis provides more definitive results, it is an invasive procedure and carries a small risk of miscarriage (less than 1%). Like NIPT, it is typically focused on identifying major chromosomal abnormalities (such as Down syndrome) or specific conditions that are already suspected. In other words, these traditional prenatal tests look for a handful of potential problems, after pregnancy has begun, rather than scanning the genome for other hidden issues.

Comparing Orchid to PGT-A to NIPT and Amniocentesis 

When comparing these genetic testing options, the key differences lie in timing and whether the test is a screening or diagnostic tool. All preimplantation genetic testing (PGT) is performed before conception (on IVF Embryos) and is considered a screening test, meaning results should be confirmed through diagnostic testing like amniocentesis during pregnancy. PGT-A and NIPT both screen for similar chromosomal conditions, but their timing differs.

Unlike traditional PGT-A, which only checks for chromosome abnormalities, Orchid’s whole-genome PGT provides a detailed genetic health report before pregnancy. It uncovers risks for:

• Subtle chromosomal abnormalities missed by PGT-A 
• Complex diseases like heart disease and diabetes
• Hundreds of single-gene disorders

By offering this comprehensive insight before implantation, Orchid allows families to move from a reactive approach (finding out about problems during pregnancy or after birth) to a proactive one—selecting an embryo with the best possible genetic start.

For parents looking to reduce the risk of unexpected genetic conditions and ensure the healthiest life for their child, Orchid represents the next evolution in reproductive genetic screening.