Overcoming challenges in variant calling : exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)

Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses

Diagnostic and prognostic correlates of preoperative FDG PET for breast cancer

Purpose: To explore the preoperative utility of FDG PET for the diagnosis and prognosis in a retrospective breast cancer case series. Methods: In this retrospective study, 104 patients who had undergone a preoperative FDG PET scan for primary breast cancer at the UZ Brussel during the period 2002-2008 were identified. Selection criteria were: histological confirmation, FDG PET performed prior to therapy, and breast surgery integrated into the primary therapy plan. Patterns of increased metabolism were recorded according to the involved locations: breast, ipsilateral axillary region, internal mammary chain, or distant organs. The end-point for the survival analysis using Cox proportional hazards was disease-free survival. The contribution of prognostic factors was evaluated using the Akaike information criterion and the Nagelkerke index. Results: PET positivity was associated with age, gender, tumour location, tumour size >2 cm, lymphovascular invasion, oestrogen and progesterone receptor status. Among 63 patients with a negative axillary PET status, 56 (88.9%) had three or fewer involved nodes, whereas among 41 patients with a positive axillary PET status, 25 (61.0%) had more than three positive nodes (P < 0.0001). In the survival analysis of preoperative characteristics, PET axillary node positivity was the foremost statistically significant factor associated with decreased disease-free survival (hazard ratio 2.81, 95% CI 1.17-6.74). Conclusion: Preoperative PET axillary node positivity identified patients with a higher burden of nodal involvement, which might be important for treatment decisions in breast cancer patient

Short course radiotherapy with simultaneous integrated boost for stage I-II breast cancer, early toxicities of a randomized clinical trial

BACKGROUND: TomoBreast is a unicenter, non-blinded randomized trial comparing conventional radiotherapy (CR) vs. hypofractionated Tomotherapy (TT) for post-operative treatment of breast cancer. The purpose of the trial is to compare whether TT can reduce heart and pulmonary toxicity. We evaluate early toxicities. METHODS: The trial started inclusion in May 2007 and reached its recruitment in August 2011. Women with stage T1-3N0M0 or T1-2N1M0 breast cancer completely resected by tumorectomy (BCS) or by mastectomy (MA) who consented to participate were randomized, according to a prescribed computer-generated randomization schedule, between control arm of CR 25x2 Gy/5 weeks by tangential fields on breast/chest wall, plus supraclavicular-axillary field if node-positive, and sequential boost 8x2 Gy/2 weeks if BCS (cumulative dose 66 Gy/7 weeks), versus experimental TT arm of 15x2.8 Gy/3 weeks, including nodal areas if node-positive and simultaneous integrated boost of 0.6 Gy if BCS (cumulative dose 51 Gy/3 weeks). Outcomes evaluated were the pulmonary and heart function. Comparison of proportions used one-sided Fisher's exact test. RESULTS: By May 2010, 70 patients were randomized and had more than 1 year of follow-up. Out of 69 evaluable cases, 32 were assigned to CR (21 BCS, 11 MA), 37 to TT (20 BCS, 17 MA). Skin toxicity of grade ≥1 at 2 years was 60% in CR, vs. 30% in TT arm. Heart function showed no significant difference for left ventricular ejection fraction at 2 years, CR 4.8% vs. TT 4.6%. Pulmonary function tests at 2 years showed grade ≥1 decline of FEV1 in 21% of CR, vs. 15% of TT and decline of DLco in 29% of CR, vs. 7% of TT (P = 0.05). CONCLUSIONS: There were no unexpected severe toxicities. Short course radiotherapy of the breast with simultaneous integrated boost over 3 weeks proved feasible without excess toxicities. Pulmonary tests showed a slight trend in favor of Tomotherapy, which will need confirmation with longer follow-up of patients. TRAIL REGISTRATION: ClinicalTrials.gov NCT0045962

Scapula alata in early breast cancer patients enrolled in a randomized clinical trial of post-surgery short-course image-guided radiotherapy

Abstract Background Scapula alata (SA) is a known complication of breast surgery associated with palsy of the serratus anterior, but it is seldom mentioned. We evaluated the risk factors associated with SA and the relationship of SA with ipsilateral shoulder/arm morbidity in a series of patients enrolled in a trial of post-surgery radiotherapy (RT). Methods The trial randomized women with completely resected stage I-II breast cancer to short-course image-guided RT, versus conventional RT. SA, arm volume and shoulder-arm mobility were measured prior to RT and at one to three months post-RT. Shoulder/arm morbidities were computed as a post-RT percentage change relative to pre-RT measurements. Results Of 119 evaluable patients, 13 (= 10.9%) had pre-RT SA. Age younger than 50 years old, a body mass index less than 25 kg/m2, and axillary lymph node dissection were significant risk factors, with odds ratios of 4.8 (P = 0.009), 6.1 (P = 0.016), and 6.1 (P = 0.005), respectively. Randomization group was not significant. At one to three months’ post-RT, mean arm volume increased by 4.1% (P = 0.036) and abduction decreased by 8.6% (P = 0.046) among SA patients, but not among non-SA patients. SA resolved in eight, persisted in five, and appeared in one patient. Conclusion The relationship of SA with lower body mass index suggests that SA might have been underestimated in overweight patients. Despite apparent resolution of SA in most patients, pre-RT SA portended an increased risk of shoulder/arm morbidity. We argue that SA warrants further investigation. Incidentally, the observation of SA occurring after RT in one patient represents the second case of post-RT SA reported in the literature. </jats:sec

Bruxelles, Jérusalem

status: publishe

TomoBreast randomized clinical trial's lung-heart outcomes and mortality through the 2020 COVID-19 pandemic: data and software

Dataset and R script to reproduce the analyses of the manuscript: Vinh-Hung V, Gorobets O, Adriaenssens N, Van Parijs H, Storme G, Verellen D, Nguyen NP, Magne N, De Ridder M. Lung-heart outcomes and mortality through the 2020 COVID-19 pandemic in a prospective cohort of breast cancer radiotherapy patients. Cancers 2022; 14(24):6241. https:// doi.org/10.3390/cancers14246241 https://www.mdpi.com/2072-6694/14/24/6241 PubMed: PMID: 36551726 PMCID: PMC9777311 Info on the variables in file "aelq6_public.R" reproduced in "aelq_2_3_readme.txt": "aelq2_base2.txt" = baseline characteristics. "aelq3.txt" = longitudinal maesurements. Variables in "aelq2_base2.txt": "aelq2_base2.txt" = baseline characteristics. # Age at randomization, years. # RTdose: cf TomoBreast papers. # 51 Gy = hypofractionated, simultaneous integrated boost # 42 Gy = hypofractionated, no boost, mastectomy cases only # 50 Gy = conventional, no boost, mastectomy cases only # 66 Gy = conventional, sequential boost # Weight kg, Height cm, # Detection 1=found by screening (senology follow-up/controle) # 2=found by symptoms (pain, palpable) # 9=unknown # Smoker 0= Not smoker # 1= Smoker # 2=ex-smoker # Mastectomy (and other binary coded) 1= yes # chemosched 0=none # 1= planned after RT (sequential) # 2= prior to RT and is finished (sequential) # 3= chemo is on-going or is planned to start with RT (concomitant) # hormonetherapy 0=no # 1=tamoxifen (nolvadex) # 2=Femara (Letrozole) # 3=zoladex # 4=tamoxifen + zoladex # Laterality 1,=Right, 2=Left, 3=Bilateral # LengthFU: length of follow-up, days from randomization "aelq3.txt" = longitudinal maesurements. # "Nr" = Case ID # "Time" in days from origin (origin =date of randomization), # if negative =before randomization # "KPS" "Weight" # "Died" "LocalRec" "Metast" "NewPrim" = binary code, 0=no, 1=yes # "fAEBreast" "fAEHeart" "fAELung" "fAEOther" # fAE = freedom from breast, heart, lung, other adverse event score # "LVEF2" = ejection fraction, % # "MacIver" = estimated cardiac strain # the following are pulmonary function tests, untransformed units # "FVC", "FEV1", "PEF", "VC", "TLC", "RV", "FRC", "Raw", "sRaw", "DLCO", # "VA", "PF" # "fDY", "fFA", "fPA" = freedom from dyspnea, from fatigue, from pain # range 0 to 100 (best) # see papers: # Van Parijs, H.; Vinh-Hung, V.; Fontaine, C.; Storme, G.; Verschraegen, C.; # Nguyen, D.M.; Adriaenssens, N.; Nguyen, N.P.; Gorobets, O.; De Ridder, M. # Cardiopulmonary-related patient-reported outcomes in a randomized clinical # trial of radiation therapy for breast cancer. BMC Cancer 2021, 21, 1177, # doi:10.1186/s12885-021-08916-z. # preprint: # Van Parijs, H.; Cecilia-Joseph, E.; Gorobets, O.; Storme, G.; # Adriaenssens, N.; Heyndrickx, B.; Verschraegen, C.; Nguyen, N.P.; # De Ridder, M.; Vinh-Hung, V. Lung-heart toxicity in a randomized # clinical trial of hypofractionated image guided radiation therapy for # breast cancer. Preprints 2022, 202212, 0214. # https://doi.org/10.20944/preprints202212.0214.v1 # # "Year" = year of the observation # example: randomized 1/1/2011, measurement done 1/31/2011, time = 30 days, # Year =2011 #Additional info on the data: Van Parijs, H.; Cecilia-Joseph, E.; Gorobets, O.; Storme, G.; Adriaenssens, N.; Heyndrickx, B.; Verschraegen, C.; Nguyen, N.P.; De Ridder, M.; Vinh-Hung, V. Lung-heart toxicity in a randomized clinical trial of hypofractionated image guided radiation therapy for breast cancer. Preprints 2022, 202212, 0214 doi: 10.20944/preprints202212.0214.v1 https://www.preprints.org/manuscript/202212.0214/v

Breast conserving treatment for breast cancer: dosimetric comparison of different non-invasive techniques for additional boost delivery

BACKGROUND: Today it is unclear which technique for delivery of an additional boost after whole breast radiotherapy for breast conserved patients should be state of the art. We present a dosimetric comparison of different non-invasive treatment techniques for additional boost delivery. METHODS: For 10 different tumor bed localizations, 7 different non-invasive treatment plans were made. Dosimetric comparison of PTV-coverage and dose to organs at risk was performed. RESULTS: The Vero system achieved an excellent PTV-coverage and at the same time could minimize the dose to the organs at risk with an average near-maximum-dose (D2) to the heart of 0.9 Gy and the average volume of ipsilateral lung receiving 5 Gy (V5) of 1.5%. The TomoTherapy modalities delivered an average D2 to the heart of 0.9 Gy for the rotational and of 2.3 Gy for the static modality and an average V5 to the ipsilateral lung of 7.3% and 2.9% respectively. A rotational technique offers an adequate conformity at the cost of more low dose spread and a larger build-up area. In most cases a 2-field technique showed acceptable PTV-coverage, but a bad conformity. Electrons often delivered a worse PTV-coverage than photons, with the planning requirements achieved only in 2 patients and with an average D2 to the heart of 2.8 Gy and an average V5 to the ipsilateral lung of 5.8%. CONCLUSIONS: We present advices which can be used as guidelines for the selection of the best individualized treatment

Breast Conserving Treatment for Breast Cancer: Dosimetric Comparison of Sequential versus Simultaneous Integrated Photon Boost

Background. Breast conserving surgery followed by whole breast irradiation is widely accepted as standard of care for early breast cancer. Addition of a boost dose to the initial tumor area further reduces local recurrences. We investigated the dosimetric benefits of a simultaneously integrated boost (SIB) compared to a sequential boost to hypofractionate the boost volume, while maintaining normofractionation on the breast. Methods. For 10 patients 4 treatment plans were deployed, 1 with a sequential photon boost, and 3 with different SIB techniques: on a conventional linear accelerator, helical TomoTherapy, and static TomoDirect. Dosimetric comparison was performed. Results. PTV-coverage was good in all techniques. Conformity was better with all SIB techniques compared to sequential boost (P = 0.0001). There was less dose spilling to the ipsilateral breast outside the PTVboost (P = 0.04). The dose to the organs at risk (OAR) was not influenced by SIB compared to sequential boost. Helical TomoTherapy showed a higher mean dose to the contralateral breast, but less than 5 Gy for each patient. Conclusions. SIB showed less dose spilling within the breast and equal dose to OAR compared to sequential boost. Both helical TomoTherapy and the conventional technique delivered acceptable dosimetry. SIB seems a safe alternative and can be implemented in clinical routine

Clinical Study Breast Conserving Treatment for Breast Cancer: Dosimetric Comparison of Sequential versus Simultaneous Integrated Photon Boost

Background. Breast conserving surgery followed by whole breast irradiation is widely accepted as standard of care for early breast cancer. Addition of a boost dose to the initial tumor area further reduces local recurrences. We investigated the dosimetric benefits of a simultaneously integrated boost (SIB) compared to a sequential boost to hypofractionate the boost volume, while maintaining normofractionation on the breast. Methods. For 10 patients 4 treatment plans were deployed, 1 with a sequential photon boost, and 3 with different SIB techniques: on a conventional linear accelerator, helical TomoTherapy, and static TomoDirect. Dosimetric comparison was performed. Results. PTV-coverage was good in all techniques. Conformity was better with all SIB techniques compared to sequential boost (P = 0.0001). There was less dose spilling to the ipsilateral breast outside the PTVboost (P = 0.04). The dose to the organs at risk (OAR) was not influenced by SIB compared to sequential boost. Helical TomoTherapy showed a higher mean dose to the contralateral breast, but less than 5 Gy for each patient. Conclusions. SIB showed less dose spilling within the breast and equal dose to OAR compared to sequential boost. Both helical TomoTherapy and the conventional technique delivered acceptable dosimetry. SIB seems a safe alternative and can be implemented in clinical routine