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Transnetyx genotyping assay results
Genotyping Assay Results, supplied by Transnetyx, used in various techniques. Bioz Stars score: 99/100, based on 2179 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/genotyping+assay+results/Automated+Genotyping/bio_rxiv__64898__2026__02__10__705109-225-11-9
Average 99 stars, based on 2179 article reviews

genotyping assay results - by Bioz Stars, 2026-09

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Genotyping Assay:

Article Title: An In Vivo Model of Echovirus-Induced Meningitis Defines the Differential Roles of Type I and Type III Interferon Signaling in Central Nervous System Infection.
Article Snippet: .. All animals used in this study were genotyped by Transnetyx, and genotyping assay results are available upon request. ..

Article Title: Type I and Type III Interferons Differentially Shape Antiviral Defense and Epithelial Integrity at the Choroid Plexus
Article Snippet: .. All animals used in this study were genotyped by Transnetyx, and genotyping assay results are available upon request. ..

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LEN-resistance mutation detection by PHG. A , Pipeline of PHG. HIV RNA is extracted from blood plasma specimen and amplified. The amplified products are then equimolarly multiplexed and sequenced using a palm-sized portable nanopore sequencer. The resultant raw-sequencing data of full-length capsid and pol gene are input to PHG's cloud platform, accessible at https://hida.usc.edu/phg , which outputs drug-resistance mutations, drug resistance, linked cross-class drug-resistance mutations, and linked cross-class drug resistance. An example of PHG's output shows a drug-resistance mutation denoted by a red circle present at 100% frequency among raw reads; while another resistance mutation is present at 33% (gray circle), and the linked cross-class resistance mutations are also present at 33%. PHG reports resistance to drugs in 5 classes: CAI, PI, NRTI, NNRTI, and INSTI, along with the resistance level, categorized as high-level resistance (h), intermediate-level resistance (i), low-level resistance (l), and potentially low-level resistance (p). Drug abbreviations are provided in . B , Two major resistance mutations, Q67H and K70R, were detected (red dot, September 2024) in the capsid region following the third LEN injection in study participant NR4574 at the Los Angeles General Medical Center. The background regimen consisted of DRV and FTR, but pharmacy records indicated that these medications were not dispensed during the periods marked by the red horizontal bars (March 2024 and April 2024). The viral loads at the time of resistance-mutation detection (September 2024) and 2 months later (November 2024) were 64 272 copies/mL and 1 249 784 copies/mL, respectively. C , Comparison of number of drug-resistance mutations detected by PHG (blue) versus standard-care genotyping (gray, Quest Diagnostics: HIV-1 Genotype and HIV-1 Integrase Genotype) among study participants at the Los Angeles General Medical Center: NI6515 (1), HO1336 (2), ZU7316 (3), LV1927 (4), OQ0202 (5), BX5409 (6), KD6313 (7), GH5866 (8), MX3923 (9), FS5399 (10), QJ2545 (11), FE5063 (12), DZ4954 (13), WG8527 (14), NW1918 (15), YF3154 (16), JP3697 (17), DA9544 (18), KG6198 (19), PL6833 (20), XT3525 (21), WU7904 (22), and NR4574 (23). D , Drug-resistance mutations (vertical solid lines) and other mutations (vertical dotted lines) within CA, PR, RT, and IN. The list of other mutations is equivalent to the panel of other mutations reported from the standard clinical care testing. PHG detected multiple drug-resistance mutations, including 2 NRTI-resistance mutations (K70T and T215D), 1 NNRTI mutation (Y181C), and 1 INSTI mutation (E157Q). Additionally, PHG identified 5 other PR mutations and 1 other RT mutation. These results were consistent with standard-care genotyping outcome for this participant. From participant NW1918, neither PHG nor standard-care testing detected any drug-resistance mutations. Both methods identified the same set of 8 other mutations, as listed in . PHG and standard-care testing commonly identified 1 NRTI-resistance mutation (M184V) and 1 NNRTI-resistance mutation (V179T) in participant FS5399. PHG detected an additional NRTI-resistance mutation, K70N, as a minority variant present at 18% prevalence. An INSTI-resistance mutation (R263K) was identified by PHG, which was not evaluated through standard-care testing, as INSTI-resistance testing was not conducted at the clinic. In participant WU7904, PHG and standard-care genotyping identified the same set of drug-resistance mutations and other mutations, with the exception of V179I. This mutation was reported by standard-care genotyping only as a mixed base (V179I/V). Abbreviations: BIC, bictegravir; CA, capsid; CAI, capsid assembly inhibitor; DRV, darunavir; DTG, dolutegravir; EVG, elvitegravir; FTC, emtricitabine; FTR, fostemsavir; HIV, human immunodeficiency virus; IN, integrase; INSTI, integrase strand transfer inhibitor; LEN, lenacapavir; NRTI, nucleoside reverse transcriptase inhibitor; NNRTI, nonnucleoside reverse transcriptase inhibitor; PHG, portable HIV genotyping; PI, protease inhibitor; PR, protease; RT, reverse transcriptase; RT-PCR, reverse-transcription polymerase chain reaction; TAF, tenofovir alafenamide.

Journal: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

Article Title: Design and Evaluation of Next-Generation HIV Genotyping for Detection of Resistance Mutations to 28 Antiretroviral Drugs Across 5 Major Classes Including Lenacapavir

doi: 10.1093/cid/ciaf458

Figure Lengend Snippet: LEN-resistance mutation detection by PHG. A , Pipeline of PHG. HIV RNA is extracted from blood plasma specimen and amplified. The amplified products are then equimolarly multiplexed and sequenced using a palm-sized portable nanopore sequencer. The resultant raw-sequencing data of full-length capsid and pol gene are input to PHG's cloud platform, accessible at https://hida.usc.edu/phg , which outputs drug-resistance mutations, drug resistance, linked cross-class drug-resistance mutations, and linked cross-class drug resistance. An example of PHG's output shows a drug-resistance mutation denoted by a red circle present at 100% frequency among raw reads; while another resistance mutation is present at 33% (gray circle), and the linked cross-class resistance mutations are also present at 33%. PHG reports resistance to drugs in 5 classes: CAI, PI, NRTI, NNRTI, and INSTI, along with the resistance level, categorized as high-level resistance (h), intermediate-level resistance (i), low-level resistance (l), and potentially low-level resistance (p). Drug abbreviations are provided in . B , Two major resistance mutations, Q67H and K70R, were detected (red dot, September 2024) in the capsid region following the third LEN injection in study participant NR4574 at the Los Angeles General Medical Center. The background regimen consisted of DRV and FTR, but pharmacy records indicated that these medications were not dispensed during the periods marked by the red horizontal bars (March 2024 and April 2024). The viral loads at the time of resistance-mutation detection (September 2024) and 2 months later (November 2024) were 64 272 copies/mL and 1 249 784 copies/mL, respectively. C , Comparison of number of drug-resistance mutations detected by PHG (blue) versus standard-care genotyping (gray, Quest Diagnostics: HIV-1 Genotype and HIV-1 Integrase Genotype) among study participants at the Los Angeles General Medical Center: NI6515 (1), HO1336 (2), ZU7316 (3), LV1927 (4), OQ0202 (5), BX5409 (6), KD6313 (7), GH5866 (8), MX3923 (9), FS5399 (10), QJ2545 (11), FE5063 (12), DZ4954 (13), WG8527 (14), NW1918 (15), YF3154 (16), JP3697 (17), DA9544 (18), KG6198 (19), PL6833 (20), XT3525 (21), WU7904 (22), and NR4574 (23). D , Drug-resistance mutations (vertical solid lines) and other mutations (vertical dotted lines) within CA, PR, RT, and IN. The list of other mutations is equivalent to the panel of other mutations reported from the standard clinical care testing. PHG detected multiple drug-resistance mutations, including 2 NRTI-resistance mutations (K70T and T215D), 1 NNRTI mutation (Y181C), and 1 INSTI mutation (E157Q). Additionally, PHG identified 5 other PR mutations and 1 other RT mutation. These results were consistent with standard-care genotyping outcome for this participant. From participant NW1918, neither PHG nor standard-care testing detected any drug-resistance mutations. Both methods identified the same set of 8 other mutations, as listed in . PHG and standard-care testing commonly identified 1 NRTI-resistance mutation (M184V) and 1 NNRTI-resistance mutation (V179T) in participant FS5399. PHG detected an additional NRTI-resistance mutation, K70N, as a minority variant present at 18% prevalence. An INSTI-resistance mutation (R263K) was identified by PHG, which was not evaluated through standard-care testing, as INSTI-resistance testing was not conducted at the clinic. In participant WU7904, PHG and standard-care genotyping identified the same set of drug-resistance mutations and other mutations, with the exception of V179I. This mutation was reported by standard-care genotyping only as a mixed base (V179I/V). Abbreviations: BIC, bictegravir; CA, capsid; CAI, capsid assembly inhibitor; DRV, darunavir; DTG, dolutegravir; EVG, elvitegravir; FTC, emtricitabine; FTR, fostemsavir; HIV, human immunodeficiency virus; IN, integrase; INSTI, integrase strand transfer inhibitor; LEN, lenacapavir; NRTI, nucleoside reverse transcriptase inhibitor; NNRTI, nonnucleoside reverse transcriptase inhibitor; PHG, portable HIV genotyping; PI, protease inhibitor; PR, protease; RT, reverse transcriptase; RT-PCR, reverse-transcription polymerase chain reaction; TAF, tenofovir alafenamide.

Article Snippet: Demographic and clinical data, including ART regimens and standard-care genotyping test results (Quest Diagnostics: HIV-1 Genotype and HIV-1 Integrase Genotype), were collected from medical records.

Techniques: Mutagenesis, Clinical Proteomics, Amplification, Sequencing, Injection, Medications, Comparison, Variant Assay, Virus, Reverse Transcription, Protease Inhibitor, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction

Linked cross-class resistance mutations and PHG's LoD and sequencing depth. A , In mSTUDY participant IK6307, who reported starting long-acting CAB and RPV treatment 3 months prior to specimen collection, 2 distinct patterns of linked NNRTI and INSTI-resistance mutations were observed: (i) K101E, Y181C, E138K, G140S, and Q148K and (ii) K101E, Y181C, G140S, and Q148K. Both mutation patterns conferred high-level resistance (red) to both of this participant's long-acting medications. High-level resistance to all 5 INSTIs and a range of resistance to all 6 NNRTIs were conferred by the observed linked mutations. The resistance level is denoted as high level (red), intermediate level (orange), and low level (brown). B , The number of resistance mutations detected by PHG, UMI-labeled method (reference), and Medaka from 15 mSTUDY specimens: OQ7034-5 (1), OQ7034-6 (2), OQ7034-7 (3), YR0424-1 (4), YR0424-2 (5), YR0424-3 (6), YR0424-4 (7), YR0424-5 (8), PE0337-1 (9), PE0337-3 (10), PE0337-6 (11), OB1189-1 (12), OB1189-2 (13), JZ1125-1 (14), and IK6307-1 (15). C , Number of total mutations relative to the HXB2 sequence with PHG's LoDs of 5% (gray), 10% (red), and 20% (blue) compared with that from the UMI-labeled reference dataset (black horizontal bar) for 11 subtype C specimens: 702010374-1 (1), 703010863-1 (2), 703011129-1 (3), 703011278-2 (4), 703011280-2 (5), 703011773-2 (6), 703011798-2 (7), 703011813-1 (8), 703011860-2 (9), 703011992-2 (10), and 705010411-2 (11). Multiple independent sequencing runs were performed on a subset of specimens by reprocessing the sample specimen through the PHG pipeline . For example, specimen 703011129-1 was processed twice and specimen 703011773-2 was processed 3 times, yielding 2 and 3 sets of results for the number of total mutations at 5%, 10%, and 20% LoDs, respectively. The reference dataset was from previously published data , which was generated using fixed-site PacBio sequencing. The number of UMI-labeled consensus sequences in the reference dataset ranged from 9 to 62 . D , Average number of total mutations and the standard deviations from 100 bootstrap experiments, each conducted at sequencing depths of 100, 200, 500, and 1000 and a LoD of 5%. In each iteration, a specified number of raw reads was randomly sampled, and the mutations that exceeded the chosen LoD were quantified. With a 5% LoD, the number of detected mutations increased as sequencing depth decreased for all 9 specimens with at least 1000 raw sequencing reads: 702010374-1 (1), 703011129-1 (2), 703011278-2 (3), 703011773-2 (4), 703011798-2 (5), 703011813-1 (6), 703011860-2 (7), 703011992-2 (8), and 705010411-2 (9). E , Average number of total mutations and the standard deviations from 100 bootstrap experiments, each performed at sequencing depths of 100, 200, 500, and 1000 and a LoD of 10%. A sequencing depth of 200 showed mutation counts comparable to those obtained at depths of 500 and 1000. The run-to-run variation in each bootstrap experiment was minimal, as indicated by small standard deviations. Abbreviations: BIC, bictegravir; CAB, cabotegravir; DOR, doravirine; DPV, dapivirine; DTG, dolutegravir; EFV, efavirenz; ETR, etravirine; EVG, elvitegravir; INSTI, integrase strand transfer inhibitor; LoD, limit of detection; NNRTI, nonnucleoside reverse transcriptase inhibitor; NVP, nevirapine; PHG, portable HIV genotyping; RAL, raltegravir; RPV, rilpivirine; UMI, unique molecular identifier; VL, viral load.

Journal: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

Article Title: Design and Evaluation of Next-Generation HIV Genotyping for Detection of Resistance Mutations to 28 Antiretroviral Drugs Across 5 Major Classes Including Lenacapavir

doi: 10.1093/cid/ciaf458

Figure Lengend Snippet: Linked cross-class resistance mutations and PHG's LoD and sequencing depth. A , In mSTUDY participant IK6307, who reported starting long-acting CAB and RPV treatment 3 months prior to specimen collection, 2 distinct patterns of linked NNRTI and INSTI-resistance mutations were observed: (i) K101E, Y181C, E138K, G140S, and Q148K and (ii) K101E, Y181C, G140S, and Q148K. Both mutation patterns conferred high-level resistance (red) to both of this participant's long-acting medications. High-level resistance to all 5 INSTIs and a range of resistance to all 6 NNRTIs were conferred by the observed linked mutations. The resistance level is denoted as high level (red), intermediate level (orange), and low level (brown). B , The number of resistance mutations detected by PHG, UMI-labeled method (reference), and Medaka from 15 mSTUDY specimens: OQ7034-5 (1), OQ7034-6 (2), OQ7034-7 (3), YR0424-1 (4), YR0424-2 (5), YR0424-3 (6), YR0424-4 (7), YR0424-5 (8), PE0337-1 (9), PE0337-3 (10), PE0337-6 (11), OB1189-1 (12), OB1189-2 (13), JZ1125-1 (14), and IK6307-1 (15). C , Number of total mutations relative to the HXB2 sequence with PHG's LoDs of 5% (gray), 10% (red), and 20% (blue) compared with that from the UMI-labeled reference dataset (black horizontal bar) for 11 subtype C specimens: 702010374-1 (1), 703010863-1 (2), 703011129-1 (3), 703011278-2 (4), 703011280-2 (5), 703011773-2 (6), 703011798-2 (7), 703011813-1 (8), 703011860-2 (9), 703011992-2 (10), and 705010411-2 (11). Multiple independent sequencing runs were performed on a subset of specimens by reprocessing the sample specimen through the PHG pipeline . For example, specimen 703011129-1 was processed twice and specimen 703011773-2 was processed 3 times, yielding 2 and 3 sets of results for the number of total mutations at 5%, 10%, and 20% LoDs, respectively. The reference dataset was from previously published data , which was generated using fixed-site PacBio sequencing. The number of UMI-labeled consensus sequences in the reference dataset ranged from 9 to 62 . D , Average number of total mutations and the standard deviations from 100 bootstrap experiments, each conducted at sequencing depths of 100, 200, 500, and 1000 and a LoD of 5%. In each iteration, a specified number of raw reads was randomly sampled, and the mutations that exceeded the chosen LoD were quantified. With a 5% LoD, the number of detected mutations increased as sequencing depth decreased for all 9 specimens with at least 1000 raw sequencing reads: 702010374-1 (1), 703011129-1 (2), 703011278-2 (3), 703011773-2 (4), 703011798-2 (5), 703011813-1 (6), 703011860-2 (7), 703011992-2 (8), and 705010411-2 (9). E , Average number of total mutations and the standard deviations from 100 bootstrap experiments, each performed at sequencing depths of 100, 200, 500, and 1000 and a LoD of 10%. A sequencing depth of 200 showed mutation counts comparable to those obtained at depths of 500 and 1000. The run-to-run variation in each bootstrap experiment was minimal, as indicated by small standard deviations. Abbreviations: BIC, bictegravir; CAB, cabotegravir; DOR, doravirine; DPV, dapivirine; DTG, dolutegravir; EFV, efavirenz; ETR, etravirine; EVG, elvitegravir; INSTI, integrase strand transfer inhibitor; LoD, limit of detection; NNRTI, nonnucleoside reverse transcriptase inhibitor; NVP, nevirapine; PHG, portable HIV genotyping; RAL, raltegravir; RPV, rilpivirine; UMI, unique molecular identifier; VL, viral load.

Techniques: Sequencing, Mutagenesis, Medications, Labeling, Generated, PacBio Sequencing, Reverse Transcription

Study design. (A) Samples: number of DNA samples provided by the 7 blood services (NHSBT, SANQUIN, NYBC, ARCLB, CBS, FRCBS, SANBS). (B) Array content: bar plot indicating the number of probes per category in the transfusion module. HLA, HEA, HPA, and HNA. (C) Genotyping: 6946 identical DNA samples were genotyped with the UBDT_PC1 Transfusion Array at Sanquin and NYBC, with 3938 of these samples also genotyped using the UKBB_v2.2 GWAS array by NHSBT. (D) QC: Heat map gives the reason for, and number of, samples failing QC for the 3 genotyping laboratories. Venn diagrams show overlap in samples that failed Axiom BP QC, gender-vs-sex discordance (sex discordant), and evidence of contamination (contamination). (E) Venn diagram showing the overlap in samples passing QC. (F) Ancestry: (left) bar plot showing genetically inferred ancestry of samples typed successfully by Sanquin and NYBC (6679 samples). EUR, AFR, AMR, SAS, EAS, OTH are shown. Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively. AFR, African; AMR, Admixed American; ARCLB, Australian Red Cross Lifeblood; Axiom BP, Axiom Best Practices; CBS, Canadian Blood Services; EAS, East Asian; EUR, European; FRCBS, Finnish Red Cross Blood Service; OTH, Other; SANBS, South African National Blood Service; SANQUIN, Sanquin Blood Supply Foundation; SAS, South Asian.

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: Study design. (A) Samples: number of DNA samples provided by the 7 blood services (NHSBT, SANQUIN, NYBC, ARCLB, CBS, FRCBS, SANBS). (B) Array content: bar plot indicating the number of probes per category in the transfusion module. HLA, HEA, HPA, and HNA. (C) Genotyping: 6946 identical DNA samples were genotyped with the UBDT_PC1 Transfusion Array at Sanquin and NYBC, with 3938 of these samples also genotyped using the UKBB_v2.2 GWAS array by NHSBT. (D) QC: Heat map gives the reason for, and number of, samples failing QC for the 3 genotyping laboratories. Venn diagrams show overlap in samples that failed Axiom BP QC, gender-vs-sex discordance (sex discordant), and evidence of contamination (contamination). (E) Venn diagram showing the overlap in samples passing QC. (F) Ancestry: (left) bar plot showing genetically inferred ancestry of samples typed successfully by Sanquin and NYBC (6679 samples). EUR, AFR, AMR, SAS, EAS, OTH are shown. Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively. AFR, African; AMR, Admixed American; ARCLB, Australian Red Cross Lifeblood; Axiom BP, Axiom Best Practices; CBS, Canadian Blood Services; EAS, East Asian; EUR, European; FRCBS, Finnish Red Cross Blood Service; OTH, Other; SANBS, South African National Blood Service; SANQUIN, Sanquin Blood Supply Foundation; SAS, South Asian.

Article Snippet: Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively.

Techniques:

Reproducibility of typing results between Sanquin and NYBC for the 6679 DNA samples of the unified data. (A) Genotype reproducibility for 20 681 biallelic probe-variant pairs included in the UBDT_PC1 array design. Reproducibility expressed as percentage of concordant genotype comparisons, and gnomAD MAF for each variant are displayed on the x- and y-axes, respectively. Blue hexagons and red dots on the central scatterplot represent the density of probes with reproducibility of ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (B) Correlation of the MAF in EUR study participants vs (non-Finnish) EUR participants from the gnomAD database for each probe-variant pair. Probes with ≥99% and <99% genotype reproducibility are shown in blue and red, respectively. Contour lines represent boundaries of statistical significance with corresponding P values calculated using the χ 2 test. (C) Genotype reproducibility for critical blood antigen types and iron homeostasis probes. Box plots show the percentage reproducibility between genotypes, split across 2 y-axes ranges to highlight high-reproducibility results (99%-100%) and broader distribution patterns (40%-99%). Data are shown for HEAs, HPAs, HNAs, and iron homeostasis variants in blue, orange, green, and red, respectively. Box plots display the median (center line), interquartile range (IQR; box), whiskers (1.5 × IQR), and outliers (black circles). Outlier variants are annotated with relevant antigen types. (D) Reproducibility between HEA types generated by the Sanquin and NYBC laboratories. The reproducibility is given as a percentage between on the y-axis for the 51 HEA types on the x-axis. Results are stratified for the 5 ancestry groups. When the bars for different ancestries are at identical values, only 1 bar is shown in the order of the legend, that is blue for EUR participants in most cases. (E) The percentage of no-type results is given on the y-axis for the 51 HEA types on the x-axis. HEA types with identical percentage of no-type results are visualized according to the principles of panel D. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; MAF, minor allele frequency; NFE, non-Finnish European; SAS, South Asian.

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: Reproducibility of typing results between Sanquin and NYBC for the 6679 DNA samples of the unified data. (A) Genotype reproducibility for 20 681 biallelic probe-variant pairs included in the UBDT_PC1 array design. Reproducibility expressed as percentage of concordant genotype comparisons, and gnomAD MAF for each variant are displayed on the x- and y-axes, respectively. Blue hexagons and red dots on the central scatterplot represent the density of probes with reproducibility of ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (B) Correlation of the MAF in EUR study participants vs (non-Finnish) EUR participants from the gnomAD database for each probe-variant pair. Probes with ≥99% and <99% genotype reproducibility are shown in blue and red, respectively. Contour lines represent boundaries of statistical significance with corresponding P values calculated using the χ 2 test. (C) Genotype reproducibility for critical blood antigen types and iron homeostasis probes. Box plots show the percentage reproducibility between genotypes, split across 2 y-axes ranges to highlight high-reproducibility results (99%-100%) and broader distribution patterns (40%-99%). Data are shown for HEAs, HPAs, HNAs, and iron homeostasis variants in blue, orange, green, and red, respectively. Box plots display the median (center line), interquartile range (IQR; box), whiskers (1.5 × IQR), and outliers (black circles). Outlier variants are annotated with relevant antigen types. (D) Reproducibility between HEA types generated by the Sanquin and NYBC laboratories. The reproducibility is given as a percentage between on the y-axis for the 51 HEA types on the x-axis. Results are stratified for the 5 ancestry groups. When the bars for different ancestries are at identical values, only 1 bar is shown in the order of the legend, that is blue for EUR participants in most cases. (E) The percentage of no-type results is given on the y-axis for the 51 HEA types on the x-axis. HEA types with identical percentage of no-type results are visualized according to the principles of panel D. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; MAF, minor allele frequency; NFE, non-Finnish European; SAS, South Asian.

Article Snippet: Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively.

Techniques: Variant Assay, Generated

Array-generated typing for HEAs. (A) Comparison of clinical and UBDT_PC1 array-based HEA-typing density. In the graph, the presence of color represents a typing result (positive or negative), and the absence of color indicates a lack of a typing result. The graph is stratified according to the ancestry of the study participants, with a top and bottom panel for each ancestry group representing the density of clinical and array typing results, respectively. EUR, AFR, AMR, SAS, EAS, and OTH ancestries are shown. The HEA systems and relevant antigen types are indicated on top of the graph, and the typing density as a percentage of the total possible types is given on the right of the graph. (B) Concordance between clinical and array-generated HEA types. Bar plots showing the number of comparisons (y-axis) per HEA type (x-axis) with concordant results obtained by both Sanquin and NYBC in green and discordant results by both Sanquin and NYBC in blue, Sanquin only in orange and NYBC only in red. Ascending and descending bars represent the number of comparisons to positive clinical or negative clinical antigen types, respectively. Bar plots show the number of comparisons on a log scale. (C) HEA typing discordances. Heat map showing the cause of the discordance (columns) between clinical and array-generated types by HEA system (rows). The number of unique discordances per system and the number per cause of discordance are given on the right and top marginal bar plots, respectively. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; OTH, other; SAS, South Asian.

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: Array-generated typing for HEAs. (A) Comparison of clinical and UBDT_PC1 array-based HEA-typing density. In the graph, the presence of color represents a typing result (positive or negative), and the absence of color indicates a lack of a typing result. The graph is stratified according to the ancestry of the study participants, with a top and bottom panel for each ancestry group representing the density of clinical and array typing results, respectively. EUR, AFR, AMR, SAS, EAS, and OTH ancestries are shown. The HEA systems and relevant antigen types are indicated on top of the graph, and the typing density as a percentage of the total possible types is given on the right of the graph. (B) Concordance between clinical and array-generated HEA types. Bar plots showing the number of comparisons (y-axis) per HEA type (x-axis) with concordant results obtained by both Sanquin and NYBC in green and discordant results by both Sanquin and NYBC in blue, Sanquin only in orange and NYBC only in red. Ascending and descending bars represent the number of comparisons to positive clinical or negative clinical antigen types, respectively. Bar plots show the number of comparisons on a log scale. (C) HEA typing discordances. Heat map showing the cause of the discordance (columns) between clinical and array-generated types by HEA system (rows). The number of unique discordances per system and the number per cause of discordance are given on the right and top marginal bar plots, respectively. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; OTH, other; SAS, South Asian.

Article Snippet: Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively.

Techniques: Generated, Comparison

Common and rare HEA types. (A) Ancestral differences in frequencies of some common HEA types, which frequently elicit alloantibody formation. Heat map with the ancestry stratified frequencies of the common MNS, Rh, FY, and JK types in the unified set of 6679 DNA samples. Heat map colors range from yellow (0%) to deep blue (100%), showing HEA-type frequencies within each ancestry group. (B) Number of HFA − samples identified in the unified set of 6679 DNA samples with those identified by Sanquin and NYBC on the x- and y-axes, respectively. True negative, false negative in Sanquin, false positive and no-type in NYBC, no-type in Sanquin, no-type in NYBC, no-type in Sanquin and NYBC, and false negative in NYBC are showing in blue, red, green, orange, brown, gray, and magenta, respectively. (C) Number of patients typed negative for 16 HFA identified in the extended unified sample set. Bar plot shows phenotype and the count of negative typing results on the x- and y-axes, respectively. Typing results concordant with clinical type, array detected and confirmed, array detected and unconfirmed, false negative array types, and no-type results are shown in purple, blue, orange, yellow, and green, respectively. (D) Concordance between clinical and array-generated results for DNA samples harboring complex Rh genotypes. A graphical representation of 8 alleles of the RHD gene, in descending order: D + ( RHD∗01 ), weak D type 1 ( RHD∗01W.1 ), weak D type 2 ( RHD∗01W.2 ), weak D type 3 ( RHD∗01W.3 ), D – ( RHD∗01N.01 ), r' S type 1 ( RHD∗03N.01 ), D pseudogene ( RHD∗08N.01 ), and DEL1 ( RHD∗01EL.01 ). Counts on the right show the number of alleles detected, confirmed by clinical type, and discordant in the extended unified sample set in black, green, and orange, respectively. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; SAS, South Asian.

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: Common and rare HEA types. (A) Ancestral differences in frequencies of some common HEA types, which frequently elicit alloantibody formation. Heat map with the ancestry stratified frequencies of the common MNS, Rh, FY, and JK types in the unified set of 6679 DNA samples. Heat map colors range from yellow (0%) to deep blue (100%), showing HEA-type frequencies within each ancestry group. (B) Number of HFA − samples identified in the unified set of 6679 DNA samples with those identified by Sanquin and NYBC on the x- and y-axes, respectively. True negative, false negative in Sanquin, false positive and no-type in NYBC, no-type in Sanquin, no-type in NYBC, no-type in Sanquin and NYBC, and false negative in NYBC are showing in blue, red, green, orange, brown, gray, and magenta, respectively. (C) Number of patients typed negative for 16 HFA identified in the extended unified sample set. Bar plot shows phenotype and the count of negative typing results on the x- and y-axes, respectively. Typing results concordant with clinical type, array detected and confirmed, array detected and unconfirmed, false negative array types, and no-type results are shown in purple, blue, orange, yellow, and green, respectively. (D) Concordance between clinical and array-generated results for DNA samples harboring complex Rh genotypes. A graphical representation of 8 alleles of the RHD gene, in descending order: D + ( RHD∗01 ), weak D type 1 ( RHD∗01W.1 ), weak D type 2 ( RHD∗01W.2 ), weak D type 3 ( RHD∗01W.3 ), D – ( RHD∗01N.01 ), r' S type 1 ( RHD∗03N.01 ), D pseudogene ( RHD∗08N.01 ), and DEL1 ( RHD∗01EL.01 ). Counts on the right show the number of alleles detected, confirmed by clinical type, and discordant in the extended unified sample set in black, green, and orange, respectively. AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; SAS, South Asian.

Article Snippet: Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively.

Techniques: Generated

Performance of transfusion module on UKBB_v2.2 array. (A) Genotype reproducibility for 17 070 biallelic probe-variant pairs included in the UKBB_v2.2 array design. Reproducibility expressed as percentage of concordant genotype comparisons, and gnomAD MAF for each variant are displayed on the x- and y-axes, respectively. Blue hexagons and red dots on the central scatterplot represent the density of probes with reproducibility ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (B) Correlation of the MAF in EUR study participants vs (non-Finnish) EUR participants from the gnomAD database for each probe-variant pair. Probes with ≥99% and <99% genotype reproducibility are shown in blue and red, respectively. Contour lines represent boundaries of statistical significance with corresponding P values calculated using the χ 2 test. (C) Concordance between clinical and array-generated HEA types for the unified samples genotyped in triplicate (n = 3791). Bar plots showing the number of comparisons (y-axis) per HEA type (x-axis) with concordant results obtained by all 3 test sites in green and discordant results by all test sites in blue, Sanquin only in orange, NYBC only in red, and NHSBT only in purple. Ascending and descending bars represent the number of comparisons to positive clinical or negative clinical antigen types, respectively. Bar plots show the number of comparisons on a log scale. EUR, European; MAF, minor allele frequency; NFE, non-Finnish European.

Journal: Blood

Article Title: Array genotyping of transfusion-relevant blood cell antigens in 6946 ancestrally diverse study participants ∗ †

doi: 10.1182/blood.2025028902

Figure Lengend Snippet: Performance of transfusion module on UKBB_v2.2 array. (A) Genotype reproducibility for 17 070 biallelic probe-variant pairs included in the UKBB_v2.2 array design. Reproducibility expressed as percentage of concordant genotype comparisons, and gnomAD MAF for each variant are displayed on the x- and y-axes, respectively. Blue hexagons and red dots on the central scatterplot represent the density of probes with reproducibility ≥99% and individual probes with <99% concordance, respectively. Marginal histograms show probe counts on a log scale. (B) Correlation of the MAF in EUR study participants vs (non-Finnish) EUR participants from the gnomAD database for each probe-variant pair. Probes with ≥99% and <99% genotype reproducibility are shown in blue and red, respectively. Contour lines represent boundaries of statistical significance with corresponding P values calculated using the χ 2 test. (C) Concordance between clinical and array-generated HEA types for the unified samples genotyped in triplicate (n = 3791). Bar plots showing the number of comparisons (y-axis) per HEA type (x-axis) with concordant results obtained by all 3 test sites in green and discordant results by all test sites in blue, Sanquin only in orange, NYBC only in red, and NHSBT only in purple. Ascending and descending bars represent the number of comparisons to positive clinical or negative clinical antigen types, respectively. Bar plots show the number of comparisons on a log scale. EUR, European; MAF, minor allele frequency; NFE, non-Finnish European.

Article Snippet: Right: heat map showing concordance between the ancestry inferred from the Sanquin and NYBC genotyping results, respectively.

Techniques: Variant Assay, Generated

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